RetrogeneDB ID: | retro_cjac_1889 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:18934422..18935876(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GPAA1 | ||
| Ensembl ID: | ENSCJAG00000021455 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1889
GCCAGCTCCAAGTCGCTTGTGCTCACCGTGCCCTGTGGCTCTGACTCTACCAACACTCAGGCTGTGGGGCTGCTGCTGGC
ACTGGCTGCCCACTTCTGGGAACAGATCTCCTAAGCCAAAGATACCATGTTCCTGGTAACAGAACATGACCTTCTGGGCA
CTGAGGCTTGGCTTGAAGCCTACCATGATGTAAATGTCACAGGCATGCAGTCATCCCCCCTGCAGGGCTGAGCTGGGACC
ATTCAGGCCACCGTGACCCTGGAGCTGAGCAGTGATGTGGTCACTAGCCTGGGGCTGTGAAGGGGTTCAACAGGCAGCTG
CCCAATCTAGACCTGCTCAATCTCTTCCAGACCTTCTGCGAGAAAGGGAACCTGCTGTGCATGCTTCAGGGCAAGCTACA
GCCCCAGGACTATACATTGTCATTGGACACACCACTGCAATGCCTGCAGATACTGCTGCTCATGGTTCCGGAGCAGGACT
CCGGCCGCCCCCACGGCTCCCATGGCCTCTTCCAGTGCTGCTGTGTGGAGGCCCTAACCCTGCGTGGCATCAGTAGCTTC
CGCCAGTACAAGTATGACCTGGTGGCAGTGGTCAAAGCTTTGGAGGGCATGCTCCGAAACTCAACCACCTCCTGGAGCGC
CTGCACCAGTCCTTCTTCCTCTACCTGCTCACACCCTCTCCCGGTTAGTTTCGGTTGGCCCCTAAGTGCCTGCCACCAGC
TTCTTGCTCCTGTCCTTGGTCTCAAGGTGCTGGAACTATGGATGCAGCTGCATGAGGCTGGAGTGGGCCTTGAGAAGCCC
TGGGGAAGGGGGCTGGCTCTGGCCCCAGTGTCCCCCTTCCCCCAGCACAGGGTGTGGGGCTGGCCTCGTTCGTGGCACCT
CTGATGATCTCACAGGCCATGGGACTGGCTTTCGATGTCCTGCCAGTGCTGGGCCAACAAGTGGCCACCCAGCACTTCCC
AGTGGCAGAGGCTGAGGTTGTAGTGCTGACACTGCTGGTGATTTACGCAGCTGGCCTGGCCCAGCCCCACACAACCCATC
AGGTGGTAAAAACACAGGCCCCAGGCAGGGGCTGGATGGCGCTGAAGCTAGTAGCTCTGCTCTACCTAACACTGCAGCTG
GGCTGCATTGCCCTCACCAACGTCTCACTGGGCTTCCTGCTGGACACCACTATGGGCAGTGCTGCTGCCCTAGCCGAGCC
TCATGGGCTACAGACCCTCTATGCTGCCTTTCTAGTGCTGACTAGCCCGGGCAGCCATGCTTTTTGGCAGCCTATTCCTG
TGGCAGGAACTGCAGGAGGTGGCACCGTCACTGGCTGCGAGCTGACAGCTCTTCCTGGCAGCACTGGCCCAGGGTGTGCT
GGAGCACCACACCTACGGTTCCCTGCTCTTCCCACTGCTGTCCCTGGGCCTCTACCCCTACTGGCTGCTTTTCTGGAATG
TGGTCTTCTGGAAG
ORF - retro_cjac_1889 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.09 % |
| Parental protein coverage: | 86.15 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | ASTESLVLTVPCGSDSTNSQAVGLLLALAAHFRGQIYWAKDIIFLVTEYDLLGTEAWLEAYHDVNVTGMQ |
| AS..SLVLTVPCGSDSTN.QAVGLLLALAAHF..QI..AKD..FLVTE.DLLGTEAWLEAYHDVNVTGMQ | |
| Retrocopy | ASSKSLVLTVPCGSDSTNTQAVGLLLALAAHFWEQIS*AKDTMFLVTEHDLLGTEAWLEAYHDVNVTGMQ |
| Parental | SSPLQGRAGAIQAAVALELSSDMVTSLDVAVEGLNGQLP-NLDLLNLFQTFCQKGGLLCTLQGKLQPQDW |
| SSPLQG.AG.IQA.V.LELSSD.VTSL.....G..G..P.NLDLLNLFQTFC.KG.LLC.LQGKLQPQD. | |
| Retrocopy | SSPLQG*AGTIQATVTLELSSDVVTSLGL-*RGSTGSCP<NLDLLNLFQTFCEKGNLLCMLQGKLQPQDY |
| Parental | T-SLDGPLQGLQMLLLMVLRQASGRPHGSHGLFLRYRVEALTLRGINSFRQYKYDLVAVGKALEGMFR-K |
| T.SLD.PLQ.LQ.LLLMV..Q.SGRPHGSHGLF....VEALTLRGI.SFRQYKYDLVAV.KALEGM.R.K | |
| Retrocopy | TLSLDTPLQCLQILLLMVPEQDSGRPHGSHGLFQCCCVEALTLRGISSFRQYKYDLVAVVKALEGMLR<K |
| Parental | LNHLLERLHQSFFLYLLP-ALSRFVSIGLYMPAAGFLLL-VLGLKALELWMQLHEAGVGLEEPRGSPGPS |
| LNHLLERLHQSFFLYLL...LSR.VS.G...PA..FLLL.VLGLK.LELWMQLHEAGVGLE.P.G..... | |
| Retrocopy | LNHLLERLHQSFFLYLLT<TLSRLVSVGP*VPATSFLLL<VLGLKVLELWMQLHEAGVGLEKPWGRGLAL |
| Parental | AQVMAPP-SQGVG-LASLVAPLLISQAMGLALYVLPVLGQHVAAQHFPVAEAEAVVLTLLAIYAAGLALP |
| A.V...P.S.G.G.LAS.VAPL.ISQAMGLA..VLPVLGQ.VA.QHFPVAEAE.VVLTLL.IYAAGLA.P | |
| Retrocopy | APVSPFP>STGCG>LASFVAPLMISQAMGLAFDVLPVLGQQVATQHFPVAEAEVVVLTLLVIYAAGLAQP |
| Parental | HNTHRVVSTQAPDRGWMALKLVALIYLALQLGCIALTNFSLGFLLAATMVPTAALAKPHGSRTLYAALLV |
| H.TH.VV.TQAP.RGWMALKLVAL.YL.LQLGCIALTN.SLGFLL..TM...AALA.PHG..TLYAA.LV | |
| Retrocopy | HTTHQVVKTQAPGRGWMALKLVALLYLTLQLGCIALTNVSLGFLLDTTMGSAAALAEPHGLQTLYAAFLV |
| Parental | LTSP-AATLFGSLFLWRELQEAPLSLAEGWQLFLAALAQGVLEHHTYGALLFPLLSLGLYPCWLLFWNVL |
| LTSP.AA.LFGSLFLW.ELQE...SLA...QLFLAALAQGVLEHHTYG.LLFPLLSLGLYP.WLLFWNV. | |
| Retrocopy | LTSP>AAMLFGSLFLWQELQEVAPSLAAS*QLFLAALAQGVLEHHTYGSLLFPLLSLGLYPYWLLFWNVV |
| Parental | FWK |
| FWK | |
| Retrocopy | FWK |
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 .00 RPM | 13 .67 RPM |
| SRP051959_heart | 0 .00 RPM | 20 .36 RPM |
| SRP051959_kidney | 0 .00 RPM | 28 .95 RPM |
| SRP051959_liver | 0 .00 RPM | 25 .26 RPM |
| SRP051959_lung | 0 .00 RPM | 19 .00 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 21 .92 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 24 .31 RPM |
| SRP051959_spleen | 0 .00 RPM | 20 .32 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1889 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1889 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1889 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000021455 | 1 retrocopy |
retro_cjac_1889 ,
|
| Dipodomys ordii | ENSDORG00000008463 | 1 retrocopy |