RetrogeneDB ID: | retro_cjac_3923 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286262.1:31092..33497(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRIM24 | ||
| Ensembl ID: | ENSCJAG00000012885 | ||
| Aliases: | None | ||
| Description: | tripartite motif containing 24 [Source:HGNC Symbol;Acc:11812] |
Retrocopy-Parental alignment summary:
>retro_cjac_3923
GAGATTCAGTTATTAGAACATAAAGAGCATAGATATCAATTTATAGAAGAAGCTTTTCAGAATCAGAAAGTGATCATAGA
TACACTAATCACCAAACTGATGGAAAAAACAAAATACATAAAATTCGCAGGAAATCAGATCCAAAACAGAATTAGTGAAG
TCAATCAAAATCAAAAGCAGGTGGAACAGGATATTAAAGTTGCTATATTTACATTGGTGGTAGAAATACATAAAAAAGGA
AAAGCTCTACTGCATCAGTTAGAGAGCCTTGCAAAAGACCATCGCATGAAACTATGCAACAACAACAGGAAGTGGCTGGA
CTTTCTAAACAATTGGAGCATGCCATGCATTTTTCTAAATGGGCAGTTTCCAGTGGCAGTAGTACAGCATTACTTTATAG
CAAAGGACTGATTACATACCGGTTGCGGCACCTCCTCCGTGCAAGATGTGATGCGTCCCCAGTGACCAACAACACCATCC
AGTTTCACTGTGATCCTAGTTTCTGGGCTCAAAATATTATCAACTTAGGTTCTTTAGTAATCGAGGATAAAGAGAGCCAG
CCACAAATGCCTAAGCAGAATCCTGTCGTGGAACAGAATTCACAGCCACCAAGTGGTTTATCATCAAACGAGTTATCCAA
GTTCCCAACACAGATCAGCCTAGCTCAATTACGGCTCCAGCATATGCAGCAACAGGTAATGGCTCAGGGGCAACAGGTGC
AGCGGAGGCCAGCACCTGTGGGTTTACCAAACCCTAGAATGCAGGGGCCCATCCAGCAACCTTCCATCTCTCATCAGCAA
CCCCCTCCACGTTTGATAAACTTTCAGAATCATAGCCCCAAACCCAATGGACCAGTTCTTCCTCCTCATTCTCAACAACT
GAGATATCCACCAAACCAGAATATACCATAACAAGCAATAAAGCCCAACCCCCTACAAATGGCTTTCTTGGCTCAAGCCA
TAAAACAGTGGCAGATCAGCAGGGGACAGGGTGACCATCAACTACCAACAGCGCATCCTCTACTCCTTCCAGCCCCGCGA
TTGCTAGTGCAGCAGGATGTAATGGAAAGGCTTTTGGTTCACCTATGATCGATTTAAGCCCACCAGTGGGAGCTTCATAT
AATCTTCCCTCTCTTCCAGATATTGACTGTTCAAATACTATTATGCTGGACAATATTGTGAGGAAAGATACTAATATAGA
TCATGGCCAGCCAAGACCACGCTCAAACAGAACGGTCCAGTCACCAAATTTATCAGTGCCATCTCCAGGCCTAGCAGGAC
CTGGTATTATGACTAATGTACACCCCTCAATAAGTTCACTTAGTGCCTCCAGCGTTGGAAGCCGAGGAAGCCCTGGCCCT
TCCAGCAAACCAGCAGAAGCTGATTCTACACACAAAGTCCCAGTGGTGACGTTGGAGCCAATTCGAATAAAACAAGAAAA
CAGTGGACCAACTGAAAATTATGATTTCCCTGTTGTTATAGTGAAGCAAGAATCAGATGAAGAATCCAGGCCTCAAAATG
CCAATTATCCAAGAAGCGTACTCACCTCCCTGCTCTTAAATAGCAGCCAGAGCTCTACTTCTGAGGAGACAGTGCTAAGA
TCAGACGCCCCTGATAGTACAGATCAACCTGGACTTCACCAGGAGAATTCCTCGAATGGAAAGTCTGAGTGGCTGGATCC
TTCCCAGAAGTCACCCCTTCACATTGGAGAGACAAGGAAAGAGGATGATCCAAATGAGGACTGGTGTGCAGGTTGCCAAA
ATGGAGGGGAACTCCTGTGCTGTGAAAAGTGCCCCAAAGTATTCCATCTTTCTTGTCATGTGCCCACATTGACAAATTTT
CCAAGTGGAGAGTGGATTTGCACTTTCTGCTGAGACTTTTCTAAACCAGAAGTTGACTATGATTGATGCTCCCAGGCACA
ACTCAGAACAAAGGAAAACTGAAGGCCTTGTTAAATTATCACCTATAGATAAAAGGAAGTGTGAGCGCCTACTTTTATTT
CTTCACTGCCATGAAAGGAGCCTGGCTTTTCAAGACCCTGTTCCTCTAACTGTGCCCGATTATTCCAAAATAATTAAAAA
TCCGATGGATTTGCCAACCATCAAGAAGAGACTACAAGAAGATTATTCCATGTACTCAAAACCTGAAGATTTTGTAGCTG
ATTTTAGATTGAGCTTTCAAAACTGTGCTCAATTCAATGAGCCTGATTCAGAAGTAGCTAATGCTGGTATAAAACTTGAA
AATTATTTTGAAGAACTTCTAAAGAACCTCTATCCAGAAAAGAGATTTCCTAAACCAGAATTCAGGAATGAATCCGAAGT
TAATAAATACAGTGATGATTCAGATGATGACTTTGTACAGCCCTGAAAGAAACGCCTCAAAAGCACTGAAGAATGACAGT
TGCTT
ORF - retro_cjac_3923 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.1 % |
| Parental protein coverage: | 77.18 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | DCQLLEHKEHRYQFIEEAFQNQKVIIDTLITKLMEKTKYIKFTGNQIQNRIIEVNQNQKQVEQDIKVAIF |
| ..QLLEHKEHRYQFIEEAFQNQKVIIDTLITKLMEKTKYIKF.GNQIQNRI.EVNQNQKQVEQDIKVAIF | |
| Retrocopy | EIQLLEHKEHRYQFIEEAFQNQKVIIDTLITKLMEKTKYIKFAGNQIQNRISEVNQNQKQVEQDIKVAIF |
| Parental | TLMVEINKKGKALLHQLESLAKDHRMKL-MQQQQEVAGLSKQLEHVMHFSKWAVSSGSSTALLYSKRLIT |
| TL.VEI.KKGKALLHQLESLAKDHRMKL.MQQQQEVAGLSKQLEH.MHFSKWAVSSGSSTALLYSK.LIT | |
| Retrocopy | TLVVEIHKKGKALLHQLESLAKDHRMKL<MQQQQEVAGLSKQLEHAMHFSKWAVSSGSSTALLYSKGLIT |
| Parental | YRLRHLLRARCDASPVTNNTIQFHCDPSFWAQNIINLGSLVIEDKESQPQMPKQNPVVEQNSQPPSGLSS |
| YRLRHLLRARCDASPVTNNTIQFHCDPSFWAQNIINLGSLVIEDKESQPQMPKQNPVVEQNSQPPSGLSS | |
| Retrocopy | YRLRHLLRARCDASPVTNNTIQFHCDPSFWAQNIINLGSLVIEDKESQPQMPKQNPVVEQNSQPPSGLSS |
| Parental | NQLSKFPTQISLAQLRLQHMQQQVMAQRQQVQRRPAPVGLPNPRMQGPIQQPSISHQQPPPRLINFQNHS |
| N.LSKFPTQISLAQLRLQHMQQQVMAQ.QQVQRRPAPVGLPNPRMQGPIQQPSISHQQPPPRLINFQNHS | |
| Retrocopy | NELSKFPTQISLAQLRLQHMQQQVMAQGQQVQRRPAPVGLPNPRMQGPIQQPSISHQQPPPRLINFQNHS |
| Parental | PKPNGPVLPPHPQQLRYPPNQNIPRQAIKPNPLQMAFLAQQAIKQWQISSGQGA-PSTTNSTSSTPSSPT |
| PKPNGPVLPPH.QQLRYPPNQNIP.QAIKPNPLQMAFLA.QAIKQWQIS.GQG..PSTTNS.SSTPSSP. | |
| Retrocopy | PKPNGPVLPPHSQQLRYPPNQNIP*QAIKPNPLQMAFLA-QAIKQWQISRGQGD<PSTTNSASSTPSSPA |
| Parental | ITSAAGYDGKAFGSPMIDLSSPVGGSYNLPSLPDIDCSSTIMLDSIVRKDTNIDHGQPRPPSNRTVQSPN |
| I.SAAG..GKAFGSPMIDLS.PVG.SYNLPSLPDIDCS.TIMLD.IVRKDTNIDHGQPRP.SNRTVQSPN | |
| Retrocopy | IASAAGCNGKAFGSPMIDLSPPVGASYNLPSLPDIDCSNTIMLDNIVRKDTNIDHGQPRPRSNRTVQSPN |
| Parental | SSVPSPGLAGPVTMTSVHPPIRSPSASSVGSRGSSGSSSKPAGADSTHKVPVVMLEPIRIKQENSGPPEN |
| .SVPSPGLAGP..MT.VHP.I.S.SASSVGSRGS.G.SSKPA.ADSTHKVPVV.LEPIRIKQENSGP.EN | |
| Retrocopy | LSVPSPGLAGPGIMTNVHPSISSLSASSVGSRGSPGPSSKPAEADSTHKVPVVTLEPIRIKQENSGPTEN |
| Parental | YDFPVVIVKQESDEESRPQNANYPRSILTSLLLNSSQSSTSEETVLRSDAPDSTGDQPGLQQENSSNGKS |
| YDFPVVIVKQESDEESRPQNANYPRS.LTSLLLNSSQSSTSEETVLRSDAPDST.DQPGL.QENSSNGKS | |
| Retrocopy | YDFPVVIVKQESDEESRPQNANYPRSVLTSLLLNSSQSSTSEETVLRSDAPDST-DQPGLHQENSSNGKS |
| Parental | EWLDPSQKSPLHVGETRKEDDPNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRD |
| EWLDPSQKSPLH.GETRKEDDPNEDWCA.CQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFC.D | |
| Retrocopy | EWLDPSQKSPLHIGETRKEDDPNEDWCAGCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFC*D |
| Parental | LSKPEVEYD-CDAPSHNSEKRKTEGL-VKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIK |
| .SKPEV.YD....P.....K.K...L.VKL.PIDKRKCERLLLFL.CHE.SLAFQDPVPLTVPDY.KIIK | |
| Retrocopy | FSKPEVDYD<LMLPGTTQNKGKLKAL<VKLSPIDKRKCERLLLFLHCHERSLAFQDPVPLTVPDYSKIIK |
| Parental | NPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYPEKRF |
| NPMDL.TIKKRLQEDYSMYSKPEDFVADFRL.FQNCA.FNEPDSEVANAGIKLENYFEELLKNLYPEKRF | |
| Retrocopy | NPMDLPTIKKRLQEDYSMYSKPEDFVADFRLSFQNCAQFNEPDSEVANAGIKLENYFEELLKNLYPEKRF |
| Parental | PKPEFRNESEDNKYSDDSDDDFVQPRKKRLKSIEERQLL |
| PKPEFRNESE.NKYSDDSDDDFVQP.KKRLKS.EE.QLL | |
| Retrocopy | PKPEFRNESEVNKYSDDSDDDFVQP*KKRLKSTEE*QLL |
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 .09 RPM | 22 .76 RPM |
| SRP051959_heart | 0 .14 RPM | 14 .40 RPM |
| SRP051959_kidney | 0 .09 RPM | 23 .05 RPM |
| SRP051959_liver | 0 .13 RPM | 14 .95 RPM |
| SRP051959_lung | 0 .36 RPM | 16 .32 RPM |
| SRP051959_lymph_node | 0 .21 RPM | 12 .85 RPM |
| SRP051959_skeletal_muscle | 0 .46 RPM | 6 .75 RPM |
| SRP051959_spleen | 0 .19 RPM | 11 .76 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3923 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3923 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3923 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 | ENSCJAG00000012885 | 1 retrocopy |
retro_cjac_3923 ,
|
| Dasypus novemcinctus | ENSDNOG00000006533 | 1 retrocopy |