RetrogeneDB ID: retro_cjac_3902

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286212.1:72149..73600(+)
• 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_3902
CATAAAGTTCTAAAGGAAATTGTCAAATGTGTTTTTCAGTCAAACTACTTTGACAGCACCCACAACCACCAGAATGGGTT
GTGTGAGGAAGAAGAGGCAACTTCAGCACCTACAGTTGAAGACCAGGTAGCTGAAGCTGAACCTGAGCCAGCAGAAGAGT
ACACTGAGCAAAATGAAGTTGAATCAACAGAGTATGTAAATAAACAGTTCATGGCAGAAACACAGTTCACCAGTGGTGAA
AAGGAGCAGGTAGATGACTGGACAGTTGAAACAGTTGAGGTGGTAAATTCACTCCAGCAGCAACCTCAGGCTGCATCCCC
TTCAGTACCACAGCCCAACTCTTTGACTAGAGTGGCTCAAGCAGATCCTCTTGTGAGAAGACAGTGAGTGCAAGACCTTA
TTGCACAGATGCAGGGACCCTATAATTTCATACAGGATTCAATGCTGGATTTTGAAAACAAGACACTTGATCCTGCCATT
ATATCTGCATAGCCTATGAATCCAGCACAAAACATAGGCATGCCCCAGCTGGTTTGCCCTCCAGATCATTCTGAATCTAG
ACTTGCTCAGCCTAATCAAGTTCCTGTACAACCAGAAGCTACACAGTTTCCTTTGGTTTCATCCACAAGTGAGGGGTATA
CAGCATCTCAACCCTTGTACCAGCCTTCTCATGCTACAGAGCAATGACCACAGAAGGAACAAATTGATCAGGTTTAGGCA
ACAATCTCTTTAAATACAGACCAGACTACAGCATCATCATCCCTTTCTGCTGCTTCTCAGCCTCAAGTATTTTTAGCTGG
GACAAGCAAACCTTTACATAGTGGTGGAATCAATGCAAATGCAGCTCCATTCCAATCCATGCAAATGGTGTTCAATAGGA
ATACCCGAGTTCCCCCTGTTAATGAACCAGCAACTTTAAAACAGCAAAATTAGTACCAGGTGAGTTATAACCAGAGCTTT
TCTAGTCAGCCTCACCAAGTAGAACAAACAGAGCTTCAGCAAGAACAGCTTCAAACAGTGGTGGGCACTTACCATTCTTG
AACTGGTGGTTCACCGGACCAGTTCCATCAAGTGACTGGTAACCACCAGCAGCCTCCTCAGCAGAACACTGAATTTCCAC
GTAGCAGTCAGCCCTATTACAATAGCCGTGGTGTTTCTCATGGAGGTTCCTGTGGTGCTAGAGGCTTGATGAATGGATAC
CGGGGCCTTGCCAAAGGATTCAGAGGAAGATATGATGGTTGCCACCCTTCATTTTCTAACACTCCAAACAGTGGTTATAC
ACAGTCTCAGTTCAATGGTCCCCAGGATTACTCTGGCTATCAACGGGATGGATATCAGCAGGATTTAAAGCAAGGCTCTG
GGCAGAGTGGACAACGGGGAGCCCCACAAGGTCAAGAGGGCCCCCAAGACTCAACAAAGAAATGCTGCAAATGAACACTT
AGCAAGCAAAT

Alignment

ORF - retro_cjac_3902 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.8 %
• Parental protein coverage: 75.12 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YKVLKEIVERVFQSNYFDSTHNHQNGLCEEEEAASAPTVEDQVAEAEPEPAEEYTEQNEVESTEYVNRQF
          .KVLKEIV..VFQSNYFDSTHNHQNGLCEEEEA.SAPTVEDQVAEAEPEPAEEYTEQNEVESTEYVN.QF
Retrocopy HKVLKEIVKCVFQSNYFDSTHNHQNGLCEEEEATSAPTVEDQVAEAEPEPAEEYTEQNEVESTEYVNKQF

Parental  MAETQFTSGEKEQVDEWTVETVEVVNSLQQQPQAASPSVPEPHSLTPVAQADPLVRRQRVQDLMAQMQGP
          MAETQFTSGEKEQVD.WTVETVEVVNSLQQQPQAASPSVP.P.SLT.VAQADPLVRRQ.VQDL.AQMQGP
Retrocopy MAETQFTSGEKEQVDDWTVETVEVVNSLQQQPQAASPSVPQPNSLTRVAQADPLVRRQ*VQDLIAQMQGP

Parental  YNFIQDSMLDFENQTLDPAIVSAQPMNPAQNMDMPQLVCPPVHSESRLAQPNQVPVQPEATQVPLVSSTS
          YNFIQDSMLDFEN.TLDPAI.SA.PMNPAQN..MPQLVCPP.HSESRLAQPNQVPVQPEATQ.PLVSSTS
Retrocopy YNFIQDSMLDFENKTLDPAIISA*PMNPAQNIGMPQLVCPPDHSESRLAQPNQVPVQPEATQFPLVSSTS

Parental  EGYTGSQPLYQPSHATEQRPQKEPIDQIQATISLNTDQTTASSSLPAASQPQVFQAGTSKPLHSSGINVN
          EGYT.SQPLYQPSHATEQ.PQKE.IDQ..ATISLNTDQTTASSSL.AASQPQVF.AGTSKPLHS.GIN.N
Retrocopy EGYTASQPLYQPSHATEQ*PQKEQIDQV*ATISLNTDQTTASSSLSAASQPQVFLAGTSKPLHSGGINAN

Parental  AAPFQSMQTVFNMNAPVPPVNEPETLKQQNQYQASYNQSFSSQPHQVEQTELQQEQLQTVVGTYH----G
          AAPFQSMQ.VFN.N..VPPVNEP.TLKQQN.YQ.SYNQSFSSQPHQVEQTELQQEQLQTVVGTYH....G
Retrocopy AAPFQSMQMVFNRNTRVPPVNEPATLKQQN*YQVSYNQSFSSQPHQVEQTELQQEQLQTVVGTYHS*TGG

Parental  SPDQSHQVTGNHQQPPQQNTGFPRSSQPYYNSRGVSRGGSRGARGLMNGYRGPANGFRGGYDGYRPSFSN
          SPDQ.HQVTGNHQQPPQQNT.FPRSSQPYYNSRGVS.GGS.GARGLMNGYRG.A.GFRG.YDG..PSFSN
Retrocopy SPDQFHQVTGNHQQPPQQNTEFPRSSQPYYNSRGVSHGGSCGARGLMNGYRGLAKGFRGRYDGCHPSFSN

Parental  TPNSGYTQSQFSAPRDYSGYQRDGYQQNFKRGSGQSGPRGAPRGR-GGPPRPNRGMPQMNTQQVN
          TPNSGYTQSQF..P.DYSGYQRDGYQQ..K.GSGQSG.RGAP.G...GPPR.N..M.QMNT.Q.N
Retrocopy TPNSGYTQSQFNGPQDYSGYQRDGYQQDLKQGSGQSGQRGAPQGQ<RGPPRLNKEMLQMNT*QAN

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	0.02 RPM	74.34 RPM
SRP051959_kidney	0.00 RPM	114.37 RPM
SRP051959_liver	0.00 RPM	78.35 RPM
SRP051959_lung	0.02 RPM	110.08 RPM
SRP051959_lymph_node	0.00 RPM	107.26 RPM
SRP051959_skeletal_muscle	0.04 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_3902 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3902 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3902 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,