Table: Duplication Summary

Summary of the phylogenetic analysis of gene families whose three or more members are residing on HOX-cluster paralogons.
For each gene family the chromosomal location and topologies (in the Newick format) of those genes are given, which arose through duplications after the invertebrates vertebrates split and before the tetrapod-fish divergence. The percentage bootstrap support of the internal branches is given with each relevant topology.
  • * Represents the non-HOX bearing chromosomes.
  • † indicates that the gene family member is positioned on a different chromosome, i.e. CACNB2 is on Hsa10 and CRYBA4 on Hsa22.
Family Name Hsa2 Hsa7 Hsa12 Hsa17 Consistency_with_HOX_Phylogeny Topology
ACCN ACCN4 ACCN3 ACCN2 ACCN1 (((12,17)2)7) 96,69
ATP5G ATP5G3 ATP5G2 ATP5G1 ((17, 2)12) 92
CACNB CACNB4 CACNB3 CACNB1 ((2,12)(17,10))† 99
CBX CBX3 CBX5 CBX1 ((17, 7) 12) 51
Collagen COL3A1,COL5A COL1A2 COL2A1 COL1A1 ((((12,17)7)2)2) 93,92,83
CRY CRYBA2 CRYBA4† CRYBA1 ((17,22)2) 99
ERBB ERBB4 EGFR ERBB3 ERBB2 (((17, 7) 2) 12) 97,98
FMNL FMNL2 FMNL3 FMNL1 Yes ((2,12)17) 100
FZD FZD7 FZD1 FZD2 ((17, 2)7) 93
GLI GLI2 GLI3 GLI1 ((7, 2)12) 99
GRB GRB14 GRB10 GRB7 ((2,7)17) 92
HH IHH SHH DHH ((7, 2)12) 97
HNRNPA HNRNPA3 HNRNPA2B1 HNRNPA1 Yes ((12, 2) 7) 98
IGFBP IGFBP2 IGFBP IGFBP1, IGFBP IGFBP6 IGFBP4 ((17, 7)2) ((7, 2)12) 99,9
INHB INHBB INHBA INHBC ((7, 2)12) 93
INTB ITGB6 ITGB5* ITGB7 ITGB3 (((3, 17)2)12) 98,99
ITGA ITGA6 ITGA7 ITGA3 Yes ((12, 2)17) 97
KCNH KCNH8* KCNH3 KCNH4 ((17,3)12) 100,96
MYL MYL1 MYL6 MYL4 ((17, 2)12) 87
NACA NACAD NACA NACA2 ((12,17)2) 99
NEUROD NEUROD1 NEUROD6 NEUROD4 NEUROD2 (((17,2)7)12)) 84100
NXPH NXPH2 NXPH1 NXPH4 NXPH3 (((2,7)12)17) 95,89
ORMDL ORMDL1 ORMDL2 ORMDL3 ((2,17)12) 60
OSBPL OSBPL6 OSBPL3 OSBPL7 ((7, 2)17) 90
PDE1 PDE1A PDE1C PDE1B ((7, 2)12) 99
PDK PDK1 PDK4 PDK2 ((17,7)2)
PLEKHA PLEKHA3 PLEKHA8 PLEKHA9 ((7,12)2) 99
PPP1R1 PPP1R1C PPP1R1A PPP1R1B ((17,2)12) 98
RAMP RAMP1 RAMP3 RAMP2 ((2,7)17) 76
RND RND3 RND1 RND2 ((17, 2)12) 99
SCRN SCRN3 SCRN1 SCRN2 ((7, 2)17) 68
SLC4A SLC4A3 SLC4A2 SLC4A1 ((7, 2)17) 85
SP Sp3 Sp4 Sp1 Sp2 Yes (((12, 2) 7) 17) 98,89
TMEM106 TMEM106B TMEM106C TMEM106A ((7,12)17) 81
TNS TNS1 TNS3 TENC1 ((2,7)12) 76,83
VAMP VAMP3* VAMP1 VAMP2 Yes ((1,12)17) 67
ZNF385 ZNF385B ZNF385D* ZNF385A ZNF385C (((3,2)12)17) 58,73
ZNFN1A ZNFN1A2 ZNFN1A1 ZNFN1A4 ZNFN1A3 (((7, 17) 2) 12) 94,90
EYA EYA3 EYA4b EYA1 EYA2 Yes (((6,8) 20) 1) 99, 76
STMN STMN1 - STMN4 , STMN3 - (((1,8) 8) 20) 52, 100
MYC MYCL MYCN MYC - - ((1,2) 8) 59, 99
MROH MROH7 - MROH5 MR MROH8 - (((20,1) 8) 8) 53, 78
STK STK24a STK25 STK26c - - ((2,13) X) 77, 98
HCK LCK - LYN BLK HCK - (((8,20) (8,1)) 98,85
DLGAP DLGAP3 - DLGAP2 DLGAP4 D - ((8,1) (20,18)) 67, 100, 71
NKAIN NKAIN1 NKAIN2b NKAIN3 NKAIN4 - ((20,8) (1,6)) 56, 99, 91
KCNQ KCNQ4 KCNQ5b KCNQ3 KCNQ2 - ((6,1)(8,20)) 99,85, 69
MATN MATN1 MATN3 MATN2 MATN4 - ((20,8) (1,2)) 74
YTHDF YTHDF2 - YTHDF3 YTHDF1 - ((20,8) 1) 78,100
XKR XKR8 - XKR6 XKR XKR7 - (((8,8) 20) 1) 70, 89, 64
MYT - MYT1L ST18 MYT1 - ((20,2) 8) 99, 100
FAM110 - FAM110C FAM110B FAM110A - ((8,20) 2) 100, 62
NCOA - NCOA1 NCOA2 NCOA3 - ((20,8) 2) 100, 100
KCNS - KCNS3 KCNS2 KCNS1 - ((20,8)2) 99

Hsa: Homo Sapien Autosome.