RetrogeneDB ID: retro_cjac_3998

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286827.1:2..1447(+)
• Located in intron of: None

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_3998
AAAGTTCTAAAGGAAATTGTCAAATGTGTTTTTCAGTCAAACTACTTTGACAGCACCCACAACCACCAGAATGGGTTGTG
TGAGGAAGGAGAGGCAACTTCAGCACCTACAGTTGAAGACCAGGTAGCTGAAGCTGAACCTGAGCCAGCAGAAGAGTACA
CTGAGCAAAATGAAGTTGAATCAACAGAGTATGTAAATAAACAGTTCATGGCAGAAACACAGTTCACCAGTGGTGAAAAG
GAGCAGGTAGATGACTGGACAGTTGAAACAGTTGAGGTGGTAAATTCACTCCAGCAGCAGCCTCAGGCTGCATCCCCTTC
AGTACCACAGCCCAACTCTTTGACTAGAGTGGCTCAAGCAGATCCTCTTGTGAGAAGACAGTGAGTGCAAGACCTTATTG
CACAGATGCAGGGACCCTATAATTTCATACAGGATTCAATGCTGGATTTTGAAAACAAGACACTTGATCTTGCCATTATA
TCTGCATAGCCTATGAATCCAGCACAAAACATGGGCATGCCCCAGCTGGTTTGCCCTCCAGATCATTCTGAATCTAGACT
TGCTCAGCCTATCAAGTTCCTGTACAACCAGAAGCTACAAGGTTCCTCTGGTGTCATCCACAAGCGAGGGGTATACGGCA
TCTCAACCCTTGCACCAGCCTTCTCATGCTACAGAGCAATGACCACAGAAGGAACCAATCGATCAGGTTCAGGCAACAAT
CTCTTTAAATACAGACCAGACTACAGCATCATCATCCCTTTCTGCTGCTTCTCAGCCTCAAGTATTTTTAGCTGGGACAA
GCAAACCTTTACATAGTGGTGGAATCAATGCAAATGCAGCTCCATTCCAATCCATGCAAATGGTGTTCAATAGGAATACC
CGAGTTCCCCCTGTTAATGAACCAGCAACGTTAAAACAGCAAAATTAGTACCAGGTGAGTTATAACCAGAACTTTTCTAG
TCAGCCTCACCAAGTAGAACAAACAGAGCTTCAGCAAGAACAGCTTCAAACAGTGGTGGGCACTTACCATTCTTGAACTG
GTGGTTCACCGGACCAGTTCCATCAAGTGACTGGTGACCACCAGCAGCCTCCTCAGCAGAACACTGAATTTCCACGTAGC
AGTCAGCCCTATTACAGTAGCCGTGGTGTTTCTCATGGAGGTTCCTGTGGTGCTAGAGGCTTGATGAATGGTACCGGGGC
CTTGCCAAAGGATTCAGAGGAAGATATGATGGTTGCCACCCTTCATTTTCTAACACTCCAAACAGTGGTTATACACAGTC
TCAGTTCAATGGTCCCCAGGATTACTCTGGCTATCAACGGGATGGATATCAGCAGGATTTAAAGCAAGGCTCTGGGCAGA
GTGGACAACGGGGAGCCCCACAAGGTCAAGAGGGCCCCCAAGACTCAACAAAGAAATGCTGCAAATGAACACTTAGCAAG
TGAAT

Alignment

ORF - retro_cjac_3998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.83 %
• Parental protein coverage: 74.96 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KVLKEIVERVFQSNYFDSTHNHQNGLCEEEEAASAPTVEDQVAEAEPEPAEEYTEQNEVESTEYVNRQFM
          KVLKEIV..VFQSNYFDSTHNHQNGLCEE.EA.SAPTVEDQVAEAEPEPAEEYTEQNEVESTEYVN.QFM
Retrocopy KVLKEIVKCVFQSNYFDSTHNHQNGLCEEGEATSAPTVEDQVAEAEPEPAEEYTEQNEVESTEYVNKQFM

Parental  AETQFTSGEKEQVDEWTVETVEVVNSLQQQPQAASPSVPEPHSLTPVAQADPLVRRQRVQDLMAQMQGPY
          AETQFTSGEKEQVD.WTVETVEVVNSLQQQPQAASPSVP.P.SLT.VAQADPLVRRQ.VQDL.AQMQGPY
Retrocopy AETQFTSGEKEQVDDWTVETVEVVNSLQQQPQAASPSVPQPNSLTRVAQADPLVRRQ*VQDLIAQMQGPY

Parental  NFIQDSMLDFENQTLDPAIVSAQPMNPAQNMDMPQLVCPPVHSESRLAQP-NQVPVQPEAT-QVPLVSST
          NFIQDSMLDFEN.TLD.AI.SA.PMNPAQNM.MPQLVCPP.HSESRLAQP..QVPVQPEAT..VPLVSST
Retrocopy NFIQDSMLDFENKTLDLAIISA*PMNPAQNMGMPQLVCPPDHSESRLAQP<YQVPVQPEAT<KVPLVSST

Parental  SEGYTGSQPLYQPSHATEQRPQKEPIDQIQATISLNTDQTTASSSLPAASQPQVFQAGTSKPLHSSGINV
          SEGYT.SQPL.QPSHATEQ.PQKEPIDQ.QATISLNTDQTTASSSL.AASQPQVF.AGTSKPLHS.GIN.
Retrocopy SEGYTASQPLHQPSHATEQ*PQKEPIDQVQATISLNTDQTTASSSLSAASQPQVFLAGTSKPLHSGGINA

Parental  NAAPFQSMQTVFNMNAPVPPVNEPETLKQQNQYQASYNQSFSSQPHQVEQTELQQEQLQTVVGTYH----
          NAAPFQSMQ.VFN.N..VPPVNEP.TLKQQN.YQ.SYNQ.FSSQPHQVEQTELQQEQLQTVVGTYH....
Retrocopy NAAPFQSMQMVFNRNTRVPPVNEPATLKQQN*YQVSYNQNFSSQPHQVEQTELQQEQLQTVVGTYHS*TG

Parental  GSPDQSHQVTGNHQQPPQQNTGFPRSSQPYYNSRGVSRGGSRGARGLMNG-YRGPANGFRGGYDGYRPSF
          GSPDQ.HQVTG.HQQPPQQNT.FPRSSQPYY.SRGVS.GGS.GARGLMNG.YRG.A.GFRG.YDG..PSF
Retrocopy GSPDQFHQVTGDHQQPPQQNTEFPRSSQPYYSSRGVSHGGSCGARGLMNG<YRGLAKGFRGRYDGCHPSF

Parental  SNTPNSGYTQSQFSAPRDYSGYQRDGYQQNFKRGSGQSGPRGAPRGR-GGPPRPNRGMPQMNTQQVN
          SNTPNSGYTQSQF..P.DYSGYQRDGYQQ..K.GSGQSG.RGAP.G...GPPR.N..M.QMNT.QVN
Retrocopy SNTPNSGYTQSQFNGPQDYSGYQRDGYQQDLKQGSGQSGQRGAPQGQ<RGPPRLNKEMLQMNT*QVN

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	113.20 RPM
SRP051959_heart	0.00 RPM	74.34 RPM
SRP051959_kidney	0.00 RPM	114.37 RPM
SRP051959_liver	0.00 RPM	78.35 RPM
SRP051959_lung	0.00 RPM	110.08 RPM
SRP051959_lymph_node	0.00 RPM	107.26 RPM
SRP051959_skeletal_muscle	0.00 RPM	43.68 RPM
SRP051959_spleen	0.00 RPM	120.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3998 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3998 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3998 has 0 orthologous retrocopies within eutheria group .

---

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 ,