From: A general scenario of Hoxgene inventory variation among major sarcopterygian lineages
Target gene | Primer name | Sequence(5'-3') | AA sequences | PL* (bp) | Notes |
---|---|---|---|---|---|
Forward primers (located at homeobox region) | |||||
PG1-PG7 | HoxF1 | TNGARYTNGARAARGARTTYCA | LELEKEFH | 125 | universal for PG1-PG7 |
PG1-PG10 | HoxF1N1 | CARACNYTNGARYTNGARAARGARTT | QTLELEKEF | 128 | universal for PG1-PG10 |
 | HoxF1N2 | CARGTNACNGARYTNGARAARGARTT | QLTELEKEF | 128 | universal for PG1-PG10 |
PG5-PG7 | HoxF7S | CARACNTAYACNMGNTAYCARAC | QTYTRYQT | 149 | universal for PG5-PG7 |
PG8-PG10 | HoxF8 | TNGARAARGARTTYYTNTTYAA | LEKEFLFN | 120 | universal for PG8-PG10 |
 | HoxF8N | TNGARYTNGARAARGARTTYYT | LELEKEFL | 125 | universal for PG8-PG10 |
PG9-PG11 | HoxF9 | DSNMGNAARAARVGNTGYCCNTA | TRKKRCPY | 164 | universal for PG9-PG11 |
PG1 | HoxF1S | AAYTTYACNACNAARCARYTNAC | NFTTKQLT | 149 | universal for PG1 |
PG2 | HoxF2S | MGGACNGCNTAYACNAAYACNCA | RTAYTNTQ | 152 | specific for PG2 |
PG3 | HoxF3S | GCNTAYACNAGYGCNCARYTNGT | AYTSAQLV | 149 | specific for PG3 |
 | HoxF3S1 | MGVCCNMGVMGVBTNGARATGGC | RPRRVEMA | 80 | specific for PG3 |
PG4 | HoxF4S | ACNGCNTAYACNMGNCARCARGT | TAYTRQQV | 152 | specific for PG4 |
PG5 | HoxF5S | GGNAARMGSGCNMGSACNGC | GKRARTA | 165 | specific for A5, B5 |
 | HoxFC5 | AARCGNTCYMGAACNAGYTAYAC | KRSRTSYT | 160 | specific for C5 |
PG8 | HoxF8S | GARAARGARTTYYTNTTYAAYCC | EKEFLFNP | 116 | specific for PG8 |
PG9 | HoxF9S | GARAARGARTTYYTNTTYAAYATG | EKEFLFNM | 116 | specific for PG9 |
PG10 | HoxF10S | AARMGNTGYCCNTAYACNAARCA | KRCPYTKH | 152 | specific for PG10 |
PG11 | HoxF11 | GARYTNGARMGNGARTTYTTYTT | ELEREFFF | 122 | specific for PG11 |
PG12 | HoxF12 | DSNMGNAARAARVGNAARCCNTA | SRKKRKPY | 164 | specific for PG12 |
 | HoxF12C | AARCCNTAYTCNAARYTNCARAT | KPYSKLQL | 149 | specific for C12 |
 | HoxF12D | AARCCNTAYACNAARCARCARAT | KPYTKQQI | 149 | specific for D12 |
 | HoxF12N1 | KCNMGVAARAARMGVAARCCSTA | SRKKRKPY | 164 | specific for PG12 |
 | HoxF12N2 | KCNMGVAARAARMGVAARCCWTA | SRKKRKPY | 164 | specific for PG12 |
 | HoxF12N3 | KCNMGVAARAARMGVAARACNTA | SRKKRKTY | 164 | specific for PG12 |
PG13 | HoxF13A | GGNMGNAARAARMGNGTNCCNTA | GRKKRVPY | 164 | specific for PG13(A,C,D) |
 | HoxF13B | GGNMGNAARAARMGNATHCCNTA | GRKKRIPY | 164 | specific for PG13(B) |
 | HoxF13A1 | CARYTRAARGARCTNGARMGNGARTA | QLKELEREY | 128 | specific for PG13(A) |
 | HoxF13B1 | CARYTRAARGARCTNGARAANGARTA | QLKELENEY | 128 | specific for PG13(B,C,D) |
Reverse primers (located at homeobox region) | |||||
PG1-PG12 | HoxR1 | TTCATNCKNCKRTTYTGRAACCA | WFQNRRMK | -- | universal for PG1-PG12 |
PG13 | HoxR13 | TTNACNCKNCKRTTYTGRAACCA | WFQNRRVK | -- | specific for PG13 |
PG14 | HoxR14 | TCNGGNGTNAGRAANCGRTTYTC | ENRFLTPE | 89 | specific for PG14, used with HoxF13A/HoxF13B |
Primers used for amplification of exon1 of Hox genes | |||||
PG1 | HoxB1(5'E1)F | GACATASTRYCNAAAGGTTGTAG | 5' UTR | 590-630 | forward primer for HoxB1 |
 | HoxB1(E1)R | TTAACYTTCATCCANTCRAANGT | TFDWMKVK | -- | reverse primer for HoxB1 |
PG2 | Hox2S(E1)F | GAATTYGAGMGRGARATHGGNTT | EFEREIGF | 270-300 | forward primer for PG2 |
 | Hox2S(E1)R | YTTYTTCTCYTTCATCCANGG | PWMKEKK | -- | reverse primer for PG2 |
PG3 | Hox3S(E1)F | ATGCARAAARCRRCNTAYTAYGA | MQKATYYD | 400-480 | forward primer for PG3 |
 | HoxC3(E1)F | ATGCAAAARGSTCYYTAYTAYGA | MQKGPYYE | 400-480 | forward primer for HoxC3 |
 | HoxA3(E1)F | GCGACCTACTAYGAYAGYTCNGC | ATYYDSSA | 390-470 | forward primer for HoxA3 |
 | HoxD3(E1)F | ATGCAGAAARCNGCYTAYTAYGA | MQKTAYYD | 400-480 | forward primer for HoxD3 |
 | Hox3S(E1)R | TCYTTCATCCANGGRAADATNTG | QIFPWMKE | -- | reverse primer for PG3 |
PG6 | HoxB6(5'E1)F | AWACTRCTAATAGCTAAASCRCT | 5' UTR | 480-510 | reverse primer for HoxB6 |
 | Hox6S(E1)R | GARTTCATCCKYTGCATCCANGG | PWMQRMNS | -- | reverse primer for PG6 |
PG7 | HoxB7(5'E1)F | CTCGTAAAACCGACACTAAAACG | 5' UTR | 440-460 | forward primer for HoxB7 |
 | Hox7S(E1)R | CATCCARGGGTADATNCGRAA | FRIYPWM | -- | reverse primer for PG7 |