RetrogeneDB ID: retro_cjac_2016

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 20:29368615..29370012(-)
• Located in intron of: ENSCJAG00000014275

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPRIN1
• Ensembl ID: ENSCJAG00000010542
• Aliases: None
• Description: None

Sequence

>retro_cjac_2016
AATGCCGTTTCTAAGTACCAGGAAGTCACAAATAATTTGGAGTTTGCAAAAGAATTACAGAGGAGTTTCATGGCACTAAG
TCAAGATATTCAGAAAACAATAAAGAAGACAGCACCTCGGGAGCAGCTTATGAGAGAAGAAGCTGAACAGAAACGTTTAA
AAACTGTACTTGAGTTACAGTATGTTTTGGACGAATTGGGAAACGACGAAGTGCGAACTGACCTGAAACAAGGTTCGAAT
GGAGTGCCTATATTGTCCGAAGAGGAATTGTCATTGTTGGATGAATTCTGTAGGTTAGTAGACCCTGAACGGGACGTGAG
CTTGAGGTTGAATGAACAGTGTGAACATGCCTCCATTCACCTGTGGGTCCTGCTGGAAGGGAAGGAAAAATCTGTATGTG
GAATCACCTGTAAAGTTCTAAAAGACATTGTCGAGTGTGTTTTTCAATGAAACTACTTTGACAGCACCCACAACCACCAG
AATGGGTTGTGTGAGGAAGAAGAGGCAGCCTCAGCACCTACAATTGAAGACCAGGTAGCTGAAGCTGAACCTGAGCCAGT
GGAAGACTACACTGAGCAAAATGAAGTTGAGTCAGCAGAGTATGTAAATAGACAGTTCATGGCAGAAACACAGTTCACCA
GTGGCGAAAAGGAGCAGGTAGATGAGTGGGCAGTTGAAACAGTTGAGGTGGTAGATTCATTCCAGCAGCAGCCTCAGGCT
TCATCCCCTTCAGTACCACAACCCCACTCTTTGACTCCTGTGGCTCAAGCAGATCCCCTTCTGAGAAGACAGCGAGTACA
GGACCTTATGGCACAAATGCAGGGTCCCTATAATTTCGTACAGGATTCAGTGCTGGATTTTGAAAACCAGACACTTGATC
CTGCCATTGTATCTGCACAGCCTGTGAGTCCAGCACAAAACATGGGCATGCCCCAGCTGGTTTGCCCTCCACTTCATTCT
GAATCTAGACTTGCTCAGCCTATCAAGTTCCTGTACAACCAGAAGCTACACGGGTTCCTCTGGTGTCATCCACAAGTGAG
GGGTATACGGCATCTCAACGCCTGTACCAGCCTTCTCCTGCTACAGAGCCACGACCACAGAAGGAACCAATTGATCAGAT
TCAGGCAACAATCTCTTTAAATACAGACCGGATTACAGCATTATGATCCCTTCCTGATGCTTCTCAGCCCCAAGTACTTC
AGGCTGGGACAAGCAAACCTTTATGTAGTGGTGGAATCAATGTAAATGCAGCTCCATTCTAATCCATGCAAACGGTGTTC
AGTATGAATGCCCCAGTTCCTCCAGTTAATGAACCAGAAACTTTAATACAGCAAACTCAGTACCAGGCCAGTTATAACCA
GAGCTTTTCTAGTCAGTCTCACCAAGTAGAACAAACA

Alignment

ORF - retro_cjac_2016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.7 %
• Parental protein coverage: 71.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DAVSKYQEVTNNLEFAKELQRSFMALSQDIQKTIKKTARREQLMREEAEQKRLKTVLELQYVLDKLGDDE
          .AVSKYQEVTNNLEFAKELQRSFMALSQDIQKTIKKTA.REQLMREEAEQKRLKTVLELQYVLD.LG.DE
Retrocopy NAVSKYQEVTNNLEFAKELQRSFMALSQDIQKTIKKTAPREQLMREEAEQKRLKTVLELQYVLDELGNDE

Parental  VRTDLKQGLNGVPILSEEELSLLDEFYKLVDPERDMSLSKRLNEQYEHASIHLWDLLEGKEKSVCGTTYK
          VRTDLKQG.NGVPILSEEELSLLDEF..LVDPERD.SL..RLNEQ.EHASIHLW.LLEGKEKSVCG.T.K
Retrocopy VRTDLKQGSNGVPILSEEELSLLDEFCRLVDPERDVSL--RLNEQCEHASIHLWVLLEGKEKSVCGITCK

Parental  VLKEIVERVFQSNYFDSTHNHQNGLCEEEEAASAPTVEDQVAEAEPEPAEEYTEQNEVESTEYVNRQFMA
          VLK.IVE.VFQ.NYFDSTHNHQNGLCEEEEAASAPT.EDQVAEAEPEP.E.YTEQNEVES.EYVNRQFMA
Retrocopy VLKDIVECVFQ*NYFDSTHNHQNGLCEEEEAASAPTIEDQVAEAEPEPVEDYTEQNEVESAEYVNRQFMA

Parental  ETQFTSGEKEQVDEWTVETVEVVNSLQQQPQAASPSVPEPHSLTPVAQADPLVRRQRVQDLMAQMQGPYN
          ETQFTSGEKEQVDEW.VETVEVV.S.QQQPQA.SPSVP.PHSLTPVAQADPL.RRQRVQDLMAQMQGPYN
Retrocopy ETQFTSGEKEQVDEWAVETVEVVDSFQQQPQASSPSVPQPHSLTPVAQADPLLRRQRVQDLMAQMQGPYN

Parental  FIQDSMLDFENQTLDPAIVSAQPMNPAQNMDMPQLVCPPVHSESRLAQP-NQVPVQPEATQVPLVSSTSE
          F.QDS.LDFENQTLDPAIVSAQP..PAQNM.MPQLVCPP.HSESRLAQP..QVPVQPEAT.VPLVSSTSE
Retrocopy FVQDSVLDFENQTLDPAIVSAQPVSPAQNMGMPQLVCPPLHSESRLAQP<YQVPVQPEATRVPLVSSTSE

Parental  GYTGSQPLYQPSHATEQRPQKEPIDQIQATISLNTDQTTASSSLPAASQPQVFQAGTSKPLHSSGINVNA
          GYT.SQ.LYQPS.ATE.RPQKEPIDQIQATISLNTD..TA..SLP.ASQPQV.QAGTSKPL.S.GINVNA
Retrocopy GYTASQRLYQPSPATEPRPQKEPIDQIQATISLNTDRITAL*SLPDASQPQVLQAGTSKPLCSGGINVNA

Parental  APFQSMQTVFNMNAPVPPVNEPETLKQQNQYQASYNQSFSSQPHQVEQT
          APF.SMQTVF.MNAPVPPVNEPETL.QQ.QYQASYNQSFSSQ.HQVEQT
Retrocopy APF*SMQTVFSMNAPVPPVNEPETLIQQTQYQASYNQSFSSQSHQVEQT

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	3.37 RPM	113.20 RPM
SRP051959_heart	2.21 RPM	74.34 RPM
SRP051959_kidney	3.28 RPM	114.37 RPM
SRP051959_liver	2.12 RPM	78.35 RPM
SRP051959_lung	3.14 RPM	110.08 RPM
SRP051959_lymph_node	3.38 RPM	107.26 RPM
SRP051959_skeletal_muscle	0.59 RPM	43.68 RPM
SRP051959_spleen	2.92 RPM	120.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2016 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2016 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2016 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010542	4 retrocopies	retro_cjac_2016 , retro_cjac_3902, retro_cjac_3987, retro_cjac_3998,