RetrogeneDB ID: retro_cjac_3987

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286475.1:71591..73497(+)
• 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_3987
GGTAAGGTTGATGATTACCAGGAACGAATGAACAAAGGGGAAAGGCTTAATCAAGATCAGCTGGATGCCGTTTCTAAGTA
CCAGGAAGTCACCAATAATTTGGAGTTTGCAAAAGAATTACAGAGGCGTTTCATGGCACTAAGTCAAGATATTCAGAAAA
CAATAAAGAAGACAGCACGTCAGGAGCACCTTATGAGAGAAGAAGCTGAACAGAAACGTTTAAAAACTGTACTTGAGCTA
CAGTATGTTTTGGACAAACTGGGAGATGATGAAGTGTGAACTGACCTGAAACAAGGTTTGAATGGAGTGCCTATATTGTC
CGAAGAGGAATTGTCATTGTTGGATGAATTCTATAATTCAACTGACCCTGAACGGGACATGAGCTTGAGGTTGAATGAAC
AGTATGAACATGCTTCCATTCACCTGTGGGACCTGCTGGAAGGGAAGGAAAAATCTGTATGTGGAACCACATAAAGTTCT
AAAGGAAATTATCGACTGTGTTCTTCAGTCAAACTACTTTGACAACACCCACAACCACCAGAATGGGTTGCGTGAGGAAG
AAGAGGCAGCCGCAGCACGTACAGTTGAAGACCAGATAGCTGAAGCTGAACCTGAGCCAGCAGAGAGTACACTGAGCAAA
ATAAAGTTGAATCCACAGAGGATGCAAATAGACAGTTCATGGCAGAAACACAGTACACCAGTGGTGAAAAGGAGCAGGTA
GATGAGTGGACAGTTGAAACAGTTGAGGTGGTAAATTCACTCCAGGAGCAACCGCAGGCTGCATCCTCTTCAGTACCGCA
GCCCCACTCTCTGACTAGAGTGGCTCAGGCAGATTCCCTTGTGAGAAGACAGTGAGTGCAAGACCTTATGGCACAGATGC
AGGGTCTGTATAATTTCATACAGAATTCAATGCTGGATTTTGAAAATGAGACACTTGATCCTGCCATTGTATCTGCACAG
CCTATGAATCCAGCACAAAACATGGACATGCCCCAGCTGGTTTGACCTCCAGTTCAGTCTGAATCTAGACTTGCTCAGCC
TAATCAAGTTCCTGTACAACCAGAAGCTACAAGGTTCCTCTGGTGTCATCCACAAGCGAGGGGTATACAGCATCTCAACC
TTTGTACCAGCCTTCTCATGCTACAGAGCAATGACCACAGAAGGAACCAATCAATCAGATTCAGGCAACAATCTCTTTAA
ATACAGACCAGACTACAGCATCATCATCCCTTTCTGCTGCTTCTCAGCCTCAAGTATTTCAGGCTGGGACAAGCAAACCT
TTACATAGTGGTGGAATTAATGCAAATGCAGCTCCATTCCAATCCATGGAAACGGTGTTCAATATGAATACCCCAGTTCC
CCCTGTTAATGAACCAGCAACTTTAAAACAGCAAAATCAGTACCAGACGAGTTATAACTAGAGCTTTTCTAGTCAGCCTC
ACCAAGTAGAAGAAACAGAGCTTCAGCAAGAACAGCTTCAAACAGTGGTGGGCACTTACCATGGTTCCCCAGACCAGTCC
CATCAAGTGATGGGAACCACCAGCAGCTTCCTCAGCGGAACAGTGGATTTCCACGTAGCAGTCAGCCCTATTACAATAGC
TGTGGTGTGTCTCATGGAGGTTCTCGTGGTGCTAGAAGCTTGATGAATGGATACCGGGGCCCTGCCAAAGGACTCAAAGG
AGGATATGATGGTTGCCACCCTTCATTCTCTAACACTCCAAACAGTGGTTATACACGATCTCAGTTCAATGCTCCCTGGG
ATTACTCTGGCTATCAACGGGTTGGATATCAGCAGAATTTCAAGCAAGGCTCTGGGCAGAGTGGACCATGGGGAGCCCCA
CAAGGTTGTGGAGGGCCCCCAAGACTCAACAGAGGGATGCTGCAAATGAACACTCAGCAAGTGAAT

Alignment

ORF - retro_cjac_3987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GKLDDYQERMNKGERLNQDQLDAVSKYQEVTNNLEFAKELQRSFMALSQDIQKTIKKTARREQLMREEAE
          GK.DDYQERMNKGERLNQDQLDAVSKYQEVTNNLEFAKELQR.FMALSQDIQKTIKKTAR.E.LMREEAE
Retrocopy GKVDDYQERMNKGERLNQDQLDAVSKYQEVTNNLEFAKELQRRFMALSQDIQKTIKKTARQEHLMREEAE

Parental  QKRLKTVLELQYVLDKLGDDEVRTDLKQGLNGVPILSEEELSLLDEFYKLVDPERDMSLSKRLNEQYEHA
          QKRLKTVLELQYVLDKLGDDEV.TDLKQGLNGVPILSEEELSLLDEFY...DPERDMSL..RLNEQYEHA
Retrocopy QKRLKTVLELQYVLDKLGDDEV*TDLKQGLNGVPILSEEELSLLDEFYNSTDPERDMSL--RLNEQYEHA

Parental  SIHLWDLLE-GKEKSVCGTTYKVLKEIVERVFQSNYFDSTHNHQNGLCEEEEAASAPTVEDQVAEAEPEP
          SIHLWDLLE.G..K.......KVLKEI...V.QSNYFD.THNHQNGL.EEEEAA.A.TVEDQ.AEAEPEP
Retrocopy SIHLWDLLE>GR-KNLYVEPHKVLKEIIDCVLQSNYFDNTHNHQNGLREEEEAAAARTVEDQIAEAEPEP

Parental  AE-EYTEQNEVESTEYVNRQFMAETQFTSGEKEQVDEWTVETVEVVNSLQQQPQAASPSVPEPHSLTPVA
          AE.EYTEQN.VESTE..NRQFMAETQ.TSGEKEQVDEWTVETVEVVNSLQ.QPQAAS.SVP.PHSLT.VA
Retrocopy AE<EYTEQNKVESTEDANRQFMAETQYTSGEKEQVDEWTVETVEVVNSLQEQPQAASSSVPQPHSLTRVA

Parental  QADPLVRRQRVQDLMAQMQGPYNFIQDSMLDFENQTLDPAIVSAQPMNPAQNMDMPQLVCPPVHSESRLA
          QAD.LVRRQ.VQDLMAQMQG.YNFIQ.SMLDFEN.TLDPAIVSAQPMNPAQNMDMPQLV.PPV.SESRLA
Retrocopy QADSLVRRQ*VQDLMAQMQGLYNFIQNSMLDFENETLDPAIVSAQPMNPAQNMDMPQLV*PPVQSESRLA

Parental  QPNQVPVQPEATQ-VPLVSSTSEGYTGSQPLYQPSHATEQRPQKEPIDQIQATISLNTDQTTASSSLPAA
          QPNQVPVQPEAT..VPLVSSTSEGYT.SQPLYQPSHATEQ.PQKEPI.QIQATISLNTDQTTASSSL.AA
Retrocopy QPNQVPVQPEATR<VPLVSSTSEGYTASQPLYQPSHATEQ*PQKEPINQIQATISLNTDQTTASSSLSAA

Parental  SQPQVFQAGTSKPLHSSGINVNAAPFQSMQTVFNMNAPVPPVNEPETLKQQNQYQASYNQSFSSQPHQVE
          SQPQVFQAGTSKPLHS.GIN.NAAPFQSM.TVFNMN.PVPPVNEP.TLKQQNQYQ.SYN.SFSSQPHQVE
Retrocopy SQPQVFQAGTSKPLHSGGINANAAPFQSMETVFNMNTPVPPVNEPATLKQQNQYQTSYN*SFSSQPHQVE

Parental  QTELQQEQLQTVVGTYHGSPDQSHQV-TGNHQQPPQQNTGFPRSSQPYYNSRGVSRGGSRGARGLMNGYR
          .TELQQEQLQTVVGTYHGSPDQSHQV..GNHQQ.PQ.N.GFPRSSQPYYNS.GVS.GGSRGAR.LMNGYR
Retrocopy ETELQQEQLQTVVGTYHGSPDQSHQV<DGNHQQLPQRNSGFPRSSQPYYNSCGVSHGGSRGARSLMNGYR

Parental  GPANGFRGGYDGYRPSFSNTPNSGYTQSQFSAPRDYSGYQRDGYQQNFKRGSGQSGPRGAPRGRGGPPRP
          GPA.G..GGYDG..PSFSNTPNSGYT.SQF.AP.DYSGYQR.GYQQNFK.GSGQSGP.GAP.G.GGPPR.
Retrocopy GPAKGLKGGYDGCHPSFSNTPNSGYTRSQFNAPWDYSGYQRVGYQQNFKQGSGQSGPWGAPQGCGGPPRL

Parental  NRGMPQMNTQQVN
          NRGM.QMNTQQVN
Retrocopy NRGMLQMNTQQVN

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	0.80 RPM	113.20 RPM
SRP051959_heart	0.79 RPM	74.34 RPM
SRP051959_kidney	1.31 RPM	114.37 RPM
SRP051959_liver	0.71 RPM	78.35 RPM
SRP051959_lung	0.94 RPM	110.08 RPM
SRP051959_lymph_node	0.91 RPM	107.26 RPM
SRP051959_skeletal_muscle	0.33 RPM	43.68 RPM
SRP051959_spleen	0.92 RPM	120.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3987 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3987 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3987 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,