RetrogeneDB ID: retro_cjac_1122

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:8767667..8769336(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EPS15L1
• Ensembl ID: ENSCJAG00000013985
• Aliases: None
• Description: None

Sequence

>retro_cjac_1122
GCTGTGAGGGTGGAAGAAAAGGCCAAATTTGATGGATATTTGAAAGCCTCTTGCCCATCAACAGTTTGCTCTTTGGAGAC
AAACTCAAGCCGGTCCTCATGAACTCAAAGCTGCCTCCTGATGTCCTGTGCCAGGTCTGGGACCTCAGTAACATCGATCA
GCATGGGCACTTGGACCGAAAAGAGTTTGCTGCGGCCATGCACTTGGTGTACCAAGCCCTTGAGAAGGAGCCCATGCCCT
CTGCCCTGCCCCCGTCCCTCATCCCACCCTCCAAGAGAAACAAGACTGCGTTCCCTGGTGCCGTCCCCGACCTGTCTGCC
AGCCCCCCACCAAAAGACAGCCTGCATGCCACACCATCCCATGGCAGCATCAACAGCCTCAGCAGCACAGGGAGACTGTC
CCCAAACACAGCCTCAAGCAAACACAGCCAACAGTGAACTGGGTGGTGCTGGTGGCAGACAAGATACGATTTGACAAGAT
ATTCCTGAAGACCGACCTGGATCTGGATGGCTGTGTGAGTGGCCAGGAGGTGAAGGAGATTTTCATGCATTTTGGCCTCA
CCCAGAACCTTCTAGCACACATATGGGCCCTAGCCAATACGAGGTAAGTGAAGAAGCTAAGCAAAGACCAATTTGCTTAG
CTGTGCATTTCATTCAGCAGAAAAGCAGTAAAGGCATCGACCCCCCTCCAGTCCTCTCACTGGACATGGTTCCACCCTCG
GAGAGAGGCACTCCTGACTCAGACAGTTCGGGCTCTCTTGGCTCCAGGGAGTTTACTGGTGTGAAGGAGCTTGAAGACAT
CAGTCAAGAGATCACCCAGTTGTAAAGAGAGAAATGTTCACTGGAACAAGACATTAGAGAAAAGGACGAGGCAATCAGAC
AGAAAACCAGCAAGGTACAGGAATTACAAAATGATTTAGACTGGGAAACAAGCAGTTTGCAAAAGCTCGAGGCTCAGAAA
CAAGACGCTCAAGACTGCCTGGACGAGATGGACTAGCAGAAGGCCGAGCTCTGAGACATGCTGAGCGATGTCTGGCAGGA
GAGCCAGGATGAGACTCAGATGATCTCATCACTGAAAACGCAAATCCAGCCTCAGGAATCTGACTTAAAGTCCCAGGAAG
ACAATCTGAACCGAGCCAAGTCGGAGCTGAAACGATTGCAGCACGAGGAAACCCAGCTGGAGCAGAGCACGCAGGCTGAG
TGAGTCCAGCTGGAAACCATCATCGAGTCCCTGAAGTCAACGCAAGACGAAATCAACCAGGCAAGGAGCAAACTTTCCCA
ACTGCACGAAAGCTGCCAGGAGGCCCACTGGAGCTGGAGCAGTATGACCAGTGCTTGACGGCGCCCACAATGCCAGCCTG
ACCGACCTGGCTGACCTGAACGAAGGCCTCCCCCGGCAAGAGGGGAAGTTTTGGAACCACGGAGGATCCTTTTGAAAATA
AAGCCTTGTTATTTAGTAACAACACTCAAGAGTTGCATCCAGATTCTTTCCAGACAGAAGACCCCTTCAAATCTGACCCA
TTTAAAGGAGCTGACCCCTCCACAGGTGACCCATTTCAGAATGACCCCTTTGCAGAACAGCAGCAGCTCCAACAGATTCA
TTTGGAGGCTCTTTCAAAGACAGCAATCCATTCCGAGGCTCCGCCACCAATGGCTGCTTCAGGAAACAA

Alignment

ORF - retro_cjac_1122 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.2 %
• Parental protein coverage: 74.34 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  AVRVEEKAKFDG-IFESLLPINGLLSGDKVKPVLMNSKLPLDVLGRVWDLSDIDKDGHLDRDEFAVAMHL
          AVRVEEKAKFDG.IFESLLPIN.LL.GDK.KPVLMNSKLP.DVL..VWDLS.ID..GHLDR.EFA.AMHL
Retrocopy AVRVEEKAKFDG<IFESLLPINSLLFGDKLKPVLMNSKLPPDVLCQVWDLSNIDQHGHLDRKEFAAAMHL

Parental  VYRALEKEPVPSALPPSLIPPSKRKKTVFPGAVPVLPASPPPKDSLRSTPSHGSVSSLNSTGSLSP-KHS
          VY.ALEKEP.PSALPPSLIPPSKR.KT.FPGAVP.L.ASPPPKDSL..TPSHGS..SL.STG.LSP.KHS
Retrocopy VYQALEKEPMPSALPPSLIPPSKRNKTAFPGAVPDLSASPPPKDSLHATPSHGSINSLSSTGRLSP<KHS

Parental  LKQTGMEPSXXWVVPVADKMRFDEIFLKTDLDLDGYVSGQEVKEIFMHSGLTQNLLAHIWALADTRQTGK
          LKQT...P...WVV.VADK.RFD.IFLKTDLDLDG.VSGQEVKEIFMH.GLTQNLLAHIWALA.TR...K
Retrocopy LKQT--QPTVNWVVLVADKIRFDKIFLKTDLDLDGCVSGQEVKEIFMHFGLTQNLLAHIWALANTR*VKK

Parental  LSKDQFA-LAMYFIQQKVSKGIDPPQVLSPDMVPPSERGTPGPDSSGSLGSGEFTGVKELDDISQEIAQL
          LSKDQFA.LA..FIQQK.SKGIDPP.VLS.DMVPPSERGTP..DSSGSLGS.EFTGVKEL.DISQEI.QL
Retrocopy LSKDQFA<LAVHFIQQKSSKGIDPPPVLSLDMVPPSERGTPDSDSSGSLGSREFTGVKELEDISQEITQL

Parental  QREKYSLEQDIREKEEAIRQKTSEVQELQNDLDRETSSLQELEAQKQDAQDRLDEMDQQKAKLRDMLSDV
          .REK.SLEQDIREK.EAIRQKTS.VQELQNDLD.ETSSLQ.LEAQKQDAQD.LDEMD.QKA.L.DMLSDV
Retrocopy *REKCSLEQDIREKDEAIRQKTSKVQELQNDLDWETSSLQKLEAQKQDAQDCLDEMD*QKAEL*DMLSDV

Parental  RQKCQDETQMISSLKTQIQSQESDLKSQEDDLNRAKSELNRLQQEETQLEQSIQAGRVQLETIIKSLKST
          .Q..QDETQMISSLKTQIQ.QESDLKSQED.LNRAKSEL.RLQ.EETQLEQS.QA..VQLETII.SLKST
Retrocopy WQESQDETQMISSLKTQIQPQESDLKSQEDNLNRAKSELKRLQHEETQLEQSTQAE*VQLETIIESLKST

Parental  QDEINQARSKLSQLHESRQEAHRS-LEQCDQ-VLDGAHATSLTDLSDLSEGVSLAERGGF-GAMDDPFKN
          QDEINQARSKLSQLHES.QEAH.S.LEQ.DQ.VLDGAH..SLTDL.DL.EG....E.G.F.G...DPF.N
Retrocopy QDEINQARSKLSQLHESCQEAHWS<LEQYDQ<VLDGAHNASLTDLADLNEGLPRQE-GKF>GTTEDPFEN

Parental  KALLFSNNTQELHPDPFQTEDPFKSDPFKGADPFKGDPFQNDPFAEQQ-TASTDPFGGDPFKESDPFRGS
          KALLFSNNTQELHPD.FQTEDPFKSDPFKGADP..GDPFQNDPFAEQQ..A.TD.FGG..FK.S.PFRGS
Retrocopy KALLFSNNTQELHPDSFQTEDPFKSDPFKGADPSTGDPFQNDPFAEQQ<AAPTDSFGGS-FKDSNPFRGS

Parental  ATEDFFKKQ
          AT...F.KQ
Retrocopy ATNGCFRKQ

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	12.82 RPM
SRP051959_heart	0.00 RPM	13.14 RPM
SRP051959_kidney	0.00 RPM	18.66 RPM
SRP051959_liver	0.00 RPM	4.48 RPM
SRP051959_lung	0.00 RPM	12.59 RPM
SRP051959_lymph_node	0.00 RPM	13.81 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.30 RPM
SRP051959_spleen	0.00 RPM	13.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1122 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1122 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1122 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002660	1 retrocopy	retro_cjac_559,
Callithrix jacchus	ENSCJAG00000007772	1 retrocopy	retro_cjac_3080,
Callithrix jacchus	ENSCJAG00000013985	1 retrocopy	retro_cjac_1122 ,
Ictidomys tridecemlineatus	ENSSTOG00000020658	2 retrocopies	retro_itri_1831, retro_itri_814,