RetrogeneDB ID: | retro_cjac_3900 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286146.1:13901..16339(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SRRM1 | ||
| Ensembl ID: | ENSCJAG00000020822 | ||
| Aliases: | None | ||
| Description: | serine/arginine repetitive matrix 1 [Source:HGNC Symbol;Acc:16638] |
Retrocopy-Parental alignment summary:
>retro_cjac_3900
ATGGACGCGGGATTCTTCCGCGGAACATGTGCAGAACAGGATAATCGGTTCAGCGACAAACAGAAGAAACTACTGAAGCA
GCTGAAATTTGCAGAATGCCTAGAAAAAAAGGTGGGCACGAGCAAAGTAAATTTGGAAGTTATAAAGCCTTGGATAACAA
AAAGAGTAACGGAAATCCGTGGGTTTAAAGATGATGTTGTGATTGAGTTTATATTCAACCAGCTGGAAGTGAAGAATCCA
GACTACAAAATGATGCAAATCAACCTGACTGGATTTTTAAACGGAAAAAATGCTCGAGAATTTATGGGAGAACTGTGGCC
CCTGCTGCTAAGTGCACAAGAAAACGTCGCGGGAATCCCTTCTGCTTTCCTAGAGCTGAAGAAAGAAGAAATAAAACAAA
GACAGATTGAACAAGAAAAATGGGCATTTATGAAAAAGCAAGATGAAGACAAAGATAAAAGGGATAAGGAAGAGAAAGAA
AGCAGCAGAGAAAAAAGGGAGAGGTCTCGTAGCCCAAGAAGACGCAAATCCAGATCTCCTTCCCCTAGAAGACGACCTTC
CCCTGTCAGGAGAGAGAGAAAGCGCAGTCATTCTCGATCTCCCGGTCACAGAACCAAGAGCCGGAGTCCTTCCCCTGCTC
CAGAAAAGAAGGAAAAAACTCCAGAGCTCCCAGAACCTTCAGTGAAAGTAAAAGAACCTTCAGTACAAGAGGCCACTTCT
ACTAGTGACATTCTGAAAGTTCCCAAACCTGAACCTGTACCAGAGCCTAAAGAACCTTCTGCAGAAAAAAATTCCAAAAA
AGAAAAGGAGAAGGAAAAGACCCGACCACGATCTCGGTCACGCTCCAAATCAAGATCCTGGACGCGGTCCCGCTCTCCTT
CTCACACTCGACCTAGATGGCACCATAGGTCTCGATCGAGATCATATTCACCTAGAAGGTGGCCAAGCCCAAGAAGGCGG
CCATCTCCTCGAAGAAGAACTCCACCAAGGAGAATGCCTCCTCCACCAAGGCATAGAAGCAGCAGATCACCAGTAAGACG
AAGAAGACGTTCGTCAGCATCCTTGTCTGGGAGTAGCTCATCATCCTCTTCATCTCGTTCCCGGTCACCACCAAAGAAAC
CGCCCAAGAGGACATCCAGCCCCCTTCGAAAAACTCGTAGGTTATCTCCTTCAGCAAGTCCTCTAAGGCGAAGGCACAGG
CCATCACCTCCTGCAACTCCACCACCCCAAACTCGGCATTCCCCAACACCCCAGCAGTCAAACTGTACAAGAAAAAGTCG
TGTTTCCATGTCTCCAGGGAGAACATCAGTAACAAAACATAAAGGTACTGAGAAAAGAGAATCCCCTTCACCAGCACCGA
AGCCTAGAAAAGTAGAGTTATCTAAATCGGAAGAAGATAAAGGTGGCAAAATGGCTGCAGCAGATTCTGTGCAGCAGAGA
CGCCAATACCGACGACAAAACCAGCAGTCTTCATCTGACTCTGGCTCCTCCTCCTCCTCACAAGATGAAAGACCCAAGAG
ATCCCATGTGAAGAATGGTGAGGTTGGCAGGCGGCGGAGACATTCCCCTTCCCAGAGTGCCTCTCCATCACCACGACAGC
GCCAAAAAGAGACTTCCCCTCGGATGCAGATGGGAAAGCGATGGCAATCGCCAGTGACTAAAAGTGGTAGACGGAGGAGA
AGTCCAACCCCACCACCCACCAGAAGGCGACGGTCTCCTTCGCCCACCCCTCCTCCTCGACAGCGCAGGTCTCCCACACC
ACCACCACGACGAAGGACTCCTTCTCCACCTCCACGTCGGCGCTCACCTTCTCCTAGAAGATATTCTCCTCCAATACAGA
GGAGATACTCTCCTTCTCCACCTCCAAAGAGAAGAACGGCTTCTCCTCCTCCCCCTCCTAAACGAAGCGCATCACCATCT
CCATCACCAAAGCATCAGGTCTCCCATTCTCCACCTCCCAAACAAAGAAGCTCCCCAGTCACCAAGAGACGTTCACCTTC
ATTATCATCCAAGCATAGGAAAGGGTCTTCCCCAAGCCGGTCTATGCGGGAGGCCCGATCACCACAACCAAACAAACGGC
ATTTGCCCTCACCACGGCCTCCAGCTCCTCAGACCTCCTCAAGTCCTCCACCTGTTCGAAGAGGAGCGTCCTCATCACCC
CAAAGAAGACAGTCCCCATCTCCAAGTACTAGGCCCATTAGGAGAGTCGCCAGGACTCCGGAACCTAAAAAGATAAAAAA
GGCTGCTTCACCAAGCCCACAGTCTGTAACAGGGTCTCATCCTCCCGATCTGTCTCTGGGTCTCCTGAGCCAACAGTTAA
AAAGCCCCCAGCACCTCCGTCCCCCATCCAGTCTCAGTCACCGCCTACAAACTGGTCACCAGCTGTACGGATCAAAAAGG
CCAAAAGCCCGACACCAAGCCCATCACCGCCAAGAAAT
ORF - retro_cjac_3900 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.92 % |
| Parental protein coverage: | 88.65 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MDAGFFRGTSAEQDNRFSNKQKKLLKQLKFAECLEKKVDMSKVNLEVIKPWITKRVTEILGFEDDVVIEF |
| MDAGFFRGT.AEQDNRFS.KQKKLLKQLKFAECLEKKV..SKVNLEVIKPWITKRVTEI.GF.DDVVIEF | |
| Retrocopy | MDAGFFRGTCAEQDNRFSDKQKKLLKQLKFAECLEKKVGTSKVNLEVIKPWITKRVTEIRGFKDDVVIEF |
| Parental | IFNQLEVKNPDSKMMQINLTGFLNGKNAREFMGELWPLLLSAQENIAGIPSAFLELKKEEIKQRQIEQEK |
| IFNQLEVKNPD.KMMQINLTGFLNGKNAREFMGELWPLLLSAQEN.AGIPSAFLELKKEEIKQRQIEQEK | |
| Retrocopy | IFNQLEVKNPDYKMMQINLTGFLNGKNAREFMGELWPLLLSAQENVAGIPSAFLELKKEEIKQRQIEQEK |
| Parental | LASMKKQDEDKDKRDKEEKESSREKRERSRSPRRRKSRSPSPRRRSSPVRRERKRSHSRSPRHRTKSRSP |
| .A.MKKQDEDKDKRDKEEKESSREKRERSRSPRRRKSRSPSPRRR.SPVRRERKRSHSRSP.HRTKSRSP | |
| Retrocopy | WAFMKKQDEDKDKRDKEEKESSREKRERSRSPRRRKSRSPSPRRRPSPVRRERKRSHSRSPGHRTKSRSP |
| Parental | SPAPEKKEKTPELPEPSVKVKEPSVQEATSTSDILKVPKPEPVPEPKEPSPEKNSKKEKEKEKTRPRSRS |
| SPAPEKKEKTPELPEPSVKVKEPSVQEATSTSDILKVPKPEPVPEPKEPS.EKNSKKEKEKEKTRPRSRS | |
| Retrocopy | SPAPEKKEKTPELPEPSVKVKEPSVQEATSTSDILKVPKPEPVPEPKEPSAEKNSKKEKEKEKTRPRSRS |
| Parental | RSKSRSRTRSRSPSHTRPRRRHRSRSRSYSPRRRPSPRRRPSPRRRTPPRRMPPPPRHRRSRSPVRRRRR |
| RSKSRS.TRSRSPSHTRPR..HRSRSRSYSPRR.PSPRRRPSPRRRTPPRRMPPPPRHR.SRSPVRRRRR | |
| Retrocopy | RSKSRSWTRSRSPSHTRPRWHHRSRSRSYSPRRWPSPRRRPSPRRRTPPRRMPPPPRHRSSRSPVRRRRR |
| Parental | SSASLSGSSSSSSSSRSRSPPKKPPKRTSSPPRKTRRLSPSASPPRRRHRPSPPATPPPKTRHSPTPQQS |
| SSASLSGSSSSSSSSRSRSPPKKPPKRTSSP.RKTRRLSPSASP.RRRHRPSPPATPPP.TRHSPTPQQS | |
| Retrocopy | SSASLSGSSSSSSSSRSRSPPKKPPKRTSSPLRKTRRLSPSASPLRRRHRPSPPATPPPQTRHSPTPQQS |
| Parental | NRTRKSRVSVSPGRTSGKVTKHKGTEKRESPSPAPKPRKVELSESEEDKGGKMAAADSVQQRRQYRRQNQ |
| N.TRKSRVS.SPGRTS..VTKHKGTEKRESPSPAPKPRKVELS.SEEDKGGKMAAADSVQQRRQYRRQNQ | |
| Retrocopy | NCTRKSRVSMSPGRTS--VTKHKGTEKRESPSPAPKPRKVELSKSEEDKGGKMAAADSVQQRRQYRRQNQ |
| Parental | QSSSDSGSSSSSEDERPKRSHVKNGEVGRRRRHSPSRSASPSPRKRQKETSPRMQMGKRWQSPVTKRFSG |
| QSSSDSGSSSSS.DERPKRSHVKNGEVGRRRRHSPS.SASPSPR.RQKETSPRMQMGKRWQSPVTK..SG | |
| Retrocopy | QSSSDSGSSSSSQDERPKRSHVKNGEVGRRRRHSPSQSASPSPRQRQKETSPRMQMGKRWQSPVTK--SG |
| Parental | RRRRSPTPPPTRRRRSPSPAPPPRRRRSPTPPPRRRTPSPPPRRRSPSPRRYSPPIQRRYSPSPPPKRRT |
| RRRRSPTPPPTRRRRSPSP.PPPR.RRSPTPPPRRRTPSPPPRRRSPSPRRYSPPIQRRYSPSPPPKRRT | |
| Retrocopy | RRRRSPTPPPTRRRRSPSPTPPPRQRRSPTPPPRRRTPSPPPRRRSPSPRRYSPPIQRRYSPSPPPKRRT |
| Parental | ASPPPPPKRRASPSPPPKHRVSHSPPPKQRSSPVTKRRSPSLSSKHRKGSSPSRSTREARSPQPNKRHSP |
| ASPPPPPKR.ASPSP.PKH.VSHSPPPKQRSSPVTKRRSPSLSSKHRKGSSPSRS.REARSPQPNKRH.P | |
| Retrocopy | ASPPPPPKRSASPSPSPKHQVSHSPPPKQRSSPVTKRRSPSLSSKHRKGSSPSRSMREARSPQPNKRHLP |
| Parental | SPRPRAPQTSSSPPPVRRGTSSSPQRRQSPSPSTRPIRRVSRTPEPKKIKKGMLPKETGDVIGHVSRINQ |
| SPRP.APQTSSSPPPVRRG.SSSPQRRQSPSPSTRPIRRV.RTPEPKKIKK...P........H...... | |
| Retrocopy | SPRPPAPQTSSSPPPVRRGASSSPQRRQSPSPSTRPIRRVARTPEPKKIKKAASPSPQSVTGSHPPDLSL |
| Parental | QSKWSRAASPSPQSIRRVSS-SRSVSGSPEPAVKKPPAPPSPIQSQSPSTN |
| ........SP..Q..R..SS.S.S......PAV....A..SP..S.SP..N | |
| Retrocopy | GLLSQQLKSP--QHLRPPSS<SQSPPTNWSPAVRIKKA-KSPTPSPSPPRN |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP051959_colon | 0 .04 RPM | 20 .48 RPM |
| SRP051959_heart | 0 .07 RPM | 27 .43 RPM |
| SRP051959_kidney | 0 .07 RPM | 36 .34 RPM |
| SRP051959_liver | 0 .15 RPM | 22 .35 RPM |
| SRP051959_lung | 0 .13 RPM | 32 .60 RPM |
| SRP051959_lymph_node | 0 .11 RPM | 35 .34 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 21 .64 RPM |
| SRP051959_spleen | 0 .08 RPM | 33 .51 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3900 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3900 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3900 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000013772 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000020822 | 2 retrocopies |
retro_cjac_1280, retro_cjac_3900 ,
|