RetrogeneDB ID: retro_cjac_1507

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:34441368..34442494(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TRIM38
• Ensembl ID: ENSCJAG00000010938
• Aliases: None
• Description: None

Sequence

>retro_cjac_1507
TATAAAATGTCATGTGAGAACATAGAGAACAGATCCACCTGCTCTGCAAAGATGAAGGACAGCTCATCTGCTGGTGCTGT
GAGCAGGCACCGTAACACAAAGGGCACACCACAGTGCTTGTTGAAGACATATGCCAGAGCTACAAGTAAAGCTCCACAAA
GTTGTGACAAATTTGAGGCAACTTGAAGACAGATGTACGGAGCAGAAGCTGTTGACGGCAATACAAATAACTAAATGAAA
GAAAAGATACAGATTCAGAGACAAAAAATTCCAGTCTGACTTTAAGGGTCTCCAGAATTTCCTACAAGAGAAAGAGAAGG
GTTATCTCTGGAGACTGGAAAAAGAATAACAACAGACTCTGAGTAGACTGAGGGACCATGAGGCCAGTCTGAGGCTGAAG
AGTGATTAACTCAAGAGCCATATCCTGGAACTGGAGGAAAAGTTCAGGGCTCAGACCAGAAATTGCTGCAGAATGTAAAT
GACACTTTGAGCAAGAGTTGGGCGGCAAAGCTGGAAACATCAGAGGCCGTCTCCTTGGAGCTTCATACTATGTGCAATGT
TTCTGAGCTTTACTTTGATGTGAAGAAAATGTTAAGGAGTCATCATGTCAGTGTGGTTCTGGATCCAGATACAGCTCATC
ATGAACTAATTCTGTCTGAAGATCAGAGACAAGTGACTCAAGGATACCCCCACTGAATCAGGACACTTCCTCCAGGAGAT
TTAGTTTCTTGCCCTGTGTCTTGGGTTGTGAAGGTTTCACCTCAGGAAGATGCTACTTTGAAGTGCATGTTAGAGAAGGA
ACTGGGTGGATTTAGGAGTTTGTATGCAAAATGTGCAAAGGGGCACTGGCATGAAGCAAGAGCCTCAGTTCCAATTCTGG
ACCCTCAGGCTGTGCAAAAAGAAAGGTTATGTAGCACTTACTTCCCCCCCAACTTCCTTTCATCTGCATGAGTAGCACCT
GGTTGTGAGAGTTTTTCTGGACTATGAGGCCGGAGTTGTATCCTTTTACAATGGGAATACTGGCTGCCACATTTTCACCT
TCCCAAAGGCTTCCTTCTCTGATATTCTCTGGCCCTATTTCCAGGTTTATCATCATTATCCTTTGCTTCTGCCTCCCCTA
GATGAT

Alignment

ORF - retro_cjac_1507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.81 %
• Parental protein coverage: 81.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  HEMSCE-EHREQLHLFCEDEGRLICWRCERAPQHKGHTTVLVEEVCQGYK-EKLQNAVTNLRQLEDRCTE
          ..MSCE.EHREQ.HL.C.DEG.LICW.CE.AP.HKGHTTVLVE..CQ.YK..KL...VTNLRQLEDRCTE
Retrocopy YKMSCE<EHREQIHLLCKDEGQLICWCCEQAP*HKGHTTVLVEDICQSYK<VKLHKVVTNLRQLEDRCTE

Parental  QKLFTAIQITK-WKEKIQIQRQKI-QSDFKSLQSFLHEEEKCYLWRLEKEEQQTLSRLRDREASLGLKSD
          QKL.TAIQITK..KEKIQIQRQKI.QSDFK.LQ.FL.E.EK.YLWRLEKE.QQTLSRLRD.EASL.LKSD
Retrocopy QKLLTAIQITK<MKEKIQIQRQKI>QSDFKGLQNFLQEKEKGYLWRLEKE*QQTLSRLRDHEASLRLKSD

Parental  ELNRHILELEEK-CQGSAQKLLQNVNDTLSRSGAVKLETSEAVSLELHTMCNVSELYFDVKKMLRSHQVS
          .L..HILELEEK..QGS.QKLLQNVNDTLS.S.A.KLETSEAVSLELHTMCNVSELYFDVKKMLRSH.VS
Retrocopy *LKSHILELEEK<VQGSDQKLLQNVNDTLSKSWAAKLETSEAVSLELHTMCNVSELYFDVKKMLRSHHVS

Parental  VTLDPDTAHHELILSEDRRQVTRGYPQ-QNQDTSSRRFSALPCVLGCEGFTSGRCYFEVDVGEGTGW-DL
          V.LDPDTAHHELILSED.RQVT.GYP...NQDTSSRRFS.LPCVLGCEGFTSGRCYFEV.V.EGTGW.DL
Retrocopy VVLDPDTAHHELILSEDQRQVTQGYPH<LNQDTSSRRFSFLPCVLGCEGFTSGRCYFEVHVREGTGW<DL

Parental  GVCVENVQRGTGMKQEPQFGFWTLRLCKKKGYVALTSPPTSLLLPEQPLVVGVFLDCEAGVVSFYNGTTG
          GVC..NVQRGTGMKQEPQF.FWTLRLCKKKGYVALTSPPTS..L.E..LVV.VFLD.EAGVVSFYNG.TG
Retrocopy GVCMQNVQRGTGMKQEPQFQFWTLRLCKKKGYVALTSPPTSFHLHE*HLVVRVFLDYEAGVVSFYNGNTG

Parental  CHIFTFPKASFSDTLRPYFQVYHYSPLFLPPLDD
          CHIFTFPKASFSD.L.PYFQVYH..PL.LPPLDD
Retrocopy CHIFTFPKASFSDILWPYFQVYHHYPLLLPPLDD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.00 RPM	10.10 RPM
SRP051959_heart	0.00 RPM	6.52 RPM
SRP051959_kidney	0.00 RPM	8.63 RPM
SRP051959_liver	0.00 RPM	5.74 RPM
SRP051959_lung	0.00 RPM	13.11 RPM
SRP051959_lymph_node	0.00 RPM	16.92 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.71 RPM
SRP051959_spleen	0.00 RPM	17.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1507 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1507 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1507 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010938	1 retrocopy	retro_cjac_1507 ,
Callithrix jacchus	ENSCJAG00000020681	1 retrocopy	retro_cjac_477,