Table 1.
Frequency of the 3′cRSS heptamer in the functional germline VH genes of 12 species.
| Species | VH family | Type of the heptamer at the 3′ end of VH genesa | References | ||
|---|---|---|---|---|---|
| TACTGTG (CACTGTG) (%) | NNNNGTG (%) | Others (%) | |||
| MAMMALS | |||||
| Mouseb (Mus musculus) | IGHV1 (J558) | 56.9 (29/51) | 94.1 (48/51) | 5.9 (3/51) | IMGT database |
| IGHV2 (Q52) | 100 (8/8) | 100 (8/8) | − | ||
| IGHV3 (36–60) | 100 (6/6) | 100 (6/6) | − | ||
| IGHV4 (X-24) | 100 (1/1) | 100 (1/1) | − | ||
| IGHV5 (7183) | 90 (9/10) | 90 (9/10) | 10 (1/10) | ||
| IGHV6 (J606) | − | − | 100 (5/5) | ||
| IGHV7 (S107) | 100 (3/3) | 100 (3/3) | − | ||
| IGHV8 (3609) | 100 (6/6) | 100 (6/6) | − | ||
| IGHV9 (VGAM3-8) | − | 100 (4/4) | − | ||
| IGHV10 (VH10) | 100 (2/2) | 100 (2/2) | − | ||
| IGHV11 (CP3) | − | − | 100 (2/2) | ||
| IGHV12 (CH27) | 100 (1/1) | 100 (1/1) | − | ||
| IGHV13 (3609N) | 50 (1/2) | 50 (1/2) | 50 (1/2) | ||
| IGHV14 (SM7) | 50 (2/4) | 50 (2/4) | 50 (2/4) | ||
| IGHV15 (VH15A) | 100 (1/1) | 100 (1/1) | − | ||
| IGHV16 | − | 100 (1/1) | − | ||
| Total | 64.5 (69/107) | 86.9 (93/107) | 13.1 (14/107) | ||
| Norway rat (Rattus norvegicus) | IGHV1 | 41.7 (10/24) | 87.5 (21/24) | 12.5 (3/24) | IMGT database |
| IGHV2 | 28.1 (9/32) | 59.4 (19/32) | 40.6 (13/32) | ||
| IGHV3 | 100 (4/4) | 100 (4/4) | − | ||
| IGHV4 | 50 (1/2) | 50 (1/2) | 50 (1/2) | ||
| IGHV5 | 71.4 (15/21) | 80.9 (17/21) | 19.1 (4/21) | ||
| IGHV6 | 12.5 (1/8) | 12.5 (1/8) | 87.5 (7/8) | ||
| IGHV7 | 66.7 (4/6) | 66.7 (4/6) | 33.3 (2/6) | ||
| IGHV8 | 87.5 (7/8) | 87.5 (7/8) | 12.5 (1/8) | ||
| IGHV9 | − | 75 (3/4) | 25 (1/4) | ||
| IGHV10 | − | − | 100 (2/2) | ||
| IGHV11 | 40 (2/5) | 40 (2/5) | 60 (3/5) | ||
| IGHV12 | − | − | 100 (1/1) | ||
| Total | 45.3 (53/117) | 67.5 (79/117) | 32.5 (38/117) | ||
| Guinea pig (Cavia porcellus) | VH1 | 90.4 (19/21) | 95.2 (20/21) | 4.8 (1/21) | Guo et al., 2012 |
| VH2 | 93.8 (15/16) | 100 (16/16) | − | ||
| VH3 | 78.8 (41/52) | 84.6 (44/52) | 15.4 (8/52) | ||
| Total | 84.3 (75/89) | 89.9 (80/89) | 10.1 (9/89) | ||
| Rabbit (Oryctolagus cuniculus) | IGHV1 | − | 100 (12/12) | − | Ros et al., 2004 |
| Total | − | 100 (12/12) | − | ||
| African elephant (Loxodonta Africana) | VH1 | 66.7 (2/3) | 66.7 (2/3) | 33.3 (1/3) | Guo et al., 2011 |
| VH2 | 100 (2/2) | 100 (2/2) | − | ||
| VH3 | 83.3 (5/6) | 83.3 (5/6) | 16.7 (1/6) | ||
| VH4 | 85.3 (29/34) | 88.2 (30/34) | 11.8 (4/34) | ||
| VH5 | 100 (2/2) | 100 (2/2) | − | ||
| VH7 | 100 (1/1) | 100 (1/1) | − | ||
| Total | 85.4 (41/48) | 87.5 (42/48) | 12.5 (6/48) | ||
| Gray short-tailed opossum (Monodelphis domestica) | VH1 | 94.7 (18/19) | 94.7 (18/19) | 5.3 (1/19) | Wang et al., 2009 |
| VH2 | − | 100 (1/1) | − | ||
| VH3 | 100 (1/1) | 100 (1/1) | − | ||
| Total | 90.5 (19/21) | 95.2 (20/21) | 4.8 (1/21) | ||
| REPTILES | |||||
| Painted turtlec (Chrysemys picta) | VH1 | 89.7 (26/29) | 96.6 (28/29) | 3.4 (1/29) | Ensembl database |
| VH2 | 10 (1/10) | 10 (1/10) | 90 (9/10) | ||
| VH3 | 100 (2/2) | 100 (2/2) | − | ||
| VH4 | − | − | 100 (1/1) | ||
| VH5 | 100 (3/3) | 100 (3/3) | − | ||
| VH6 | − | − | 100 (2/2) | ||
| VH7 | 50 (3/6) | 50 (3/6) | 50 (3/6) | ||
| VH8 | 100 (1/1) | 100 (1/1) | − | ||
| VH9 | 75 (3/4) | 75 (3/4) | 25 (1/4) | ||
| VH10 | 100 (9/9) | 100 (9/9) | − | ||
| VH11 | − | 100 (1/1) | − | ||
| Total | 70.6 (48/68) | 75 (51/68) | 25 (17/68) | ||
| Anole lizardd (Anolis carolinensis) | Group I | 46.7 (7/15) | 86.7 (13/15) | 13.3 (2/15) | Ensembl database |
| Group II | 35.3 (6/17) | 76.5 (13/17) | 23.5 (4/17) | ||
| Group III | 53.3 (8/15) | 80 (12/15) | 20 (3/15) | ||
| Group IV | 65 (13/20) | 100 (20/20) | − | ||
| Ac VH38265 | 100 (1/1) | 100 (1/1) | − | ||
| Ac VH338184 | 100 (1/1) | 100 (1/1) | − | ||
| Ac VH377057 | − | − | 100 (1/1) | ||
| Ac VH405628 | − | − | 100 (1/1) | ||
| Total | 50.7 (36/71) | 84.5 (60/71) | 15.5 (11/71) | ||
| AMPHIBIANS | |||||
| Western clawed froge (Xenopus tropicalis) | VH1 | 90.9 (10/11) | 100 (11/11) | − | Ensembl database |
| VH2 | 83.3 (5/6) | 83.3 (5/6) | 16.7 (1/6) | ||
| VH3 | − | 20 (1/5) | 80 (4/5) | ||
| VH4 | 50 (1/2) | 100 (2/2) | − | ||
| VH5 | 100 (3/3) | 100 (3/3) | − | ||
| VH6 | 100 (1/1) | 100 (1/1) | − | ||
| VH8 | 100 (6/6) | 100 (6/6) | − | ||
| VH9 | − | 100 (1/1) | − | ||
| VH10 | 100 (1/1) | 100 (1/1) | − | ||
| VH11 | 100 (2/2) | 100 (2/2) | − | ||
| Total | 76.3 (29/38) | 86.8 (33/38) | 13.2 (5/38) | ||
| TELEOSTS | |||||
| Zebrafish (Danio rerio) | IGHV1 | 100 (4/4) | 100 (4/4) | − | Danilova et al., 2005 |
| IGHV2 | 100 (3/3) | 100 (3/3) | − | ||
| IGHV3 | − | 100 (1/1) | − | ||
| IGHV4 | 85.7 (6/7) | 85.7 (6/7) | 14.3 (1/7) | ||
| IGHV5 | − | 66.7 (2/3) | 33.3 (1/3) | ||
| IGHV6 | 100 (1/1) | 100 (1/1) | − | ||
| IGHV7 | 100 (1/1) | 100 (1/1) | − | ||
| IGHV8 | 75 (3/4) | 100 (4/4) | − | ||
| IGHV9 | 50 (2/4) | 50 (2/4) | 50 (2/4) | ||
| IGHV10 | − | 100 (1/1) | − | ||
| IGHV11 | 100 (2/2) | 100 (2/2) | − | ||
| IGHV13 | − | 100 (1/1) | − | ||
| IGHV14 | 100 (1/1) | 100 (1/1) | − | ||
| Total | 69.7 (23/33) | 87.9 (29/33) | 12.1 (4/33) | ||
| Atlantic salmon (Salmo salar) | IGHV1 | 63.6 (7/11) | 100 (11/11) | − | Yasuike et al., 2010 |
| IGHV2 | 100 (3/3) | 100 (3/3) | − | ||
| IGHV3 | − | 100 (1/1) | − | ||
| IGHV4 | − | 80 (4/5) | 20 (1/5) | ||
| IGHV6 | 12.5 (1/8) | 100 (8/8) | − | ||
| IGHV7 | 100 (2/2) | 100 (2/2) | − | ||
| IGHV8 | 100 (10/10) | 100 (10/10) | − | ||
| IGHV9 | − | 100 (1/1) | − | ||
| IGHV10 | 100 (1/1) | 100 (1/1) | − | ||
| IGHV12 | 100 (1/1) | 100 (1/1) | − | ||
| IGHV15 | 100 (2/2) | 100 (2/2) | − | ||
| IGHV16 | 100 (4/4) | 100 (4/4) | − | ||
| IGHV17 | − | 100 (1/1) | − | ||
| Total | 62 (31/50) | 98 (49/50) | 2 (1/50) | ||
| Channel catfish (Ictalurus punctatus) | VH1 | 100 (2/2) | 100 (2/2) | − | Bengten et al., 2006 |
| VH2 | − | − | 100 (1/1) | ||
| VH3 | 20 (1/5) | 20 (1/5) | 80 (4/5) | ||
| VH5 | − | − | 100 (1/1) | ||
| VH6 | − | − | 100 (2/2) | ||
| VH7 | − | − | 100 (5/5) | ||
| VH9 | 100 (1/1) | 100 (1/1) | − | ||
| VH11 | − | 50 (1/2) | 50 (1/2) | ||
| VH12 | − | − | 100 (2/2) | ||
| VH14 | 100 (1/1) | 100 (1/1) | − | ||
| Total | 22.7 (5/22) | 27.3 (6/22) | 72.7 (16/22) | ||
The denominator inside the parentheses represents the total number of functional VH genes in the corresponding VH family, and the numerator represents the number of functional VH genes that contain the specified type of heptamer in the corresponding VH family. If a VH gene had more than one allele, only the 01 allele was used in the analysis of the 3′cRSS.
All of the functional VH genes were obtained from the VH repertoire of the C57BL/6 strain (imgt.org/IMGTrepertoire).
The functional germline VH genes of the painted turtle were identified from the genome scaffolds JH585110, JH585065, and JH585278 (pre.ensembl.org/Chrysemys_picta_bellii).
The functional germline VH genes of the anole lizard were identified from the genome scaffold GL343491 (ensembl.org/Anolis_carolinensis). The groups of the anole lizard VH genes are classified according to the phylogenetic study by Gambon Deza et al. (2009). Ac VH338184, Ac VH377057, and Ac VH405628 are three functional germline VH genes that are not included in the following phylogenetic analysis.