RetrogeneDB ID: retro_cjac_3080

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:70979299..70981125(+)
• Located in intron of: ENSCJAG00000005976

Retrocopy information

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

Parental gene information

• Parental gene symbol: ITSN2
• Ensembl ID: ENSCJAG00000007772
• Aliases: None
• Description: None

Sequence

>retro_cjac_3080
GGAGGGCCAAACATGTGGGCTATTACCTCTGAAGAAAGTACTAAGCATGACAGGCAGTTTGATAACCTCAAACCTTCAGG
AGGTTACATAACAGGTGATCAAGCACATAATTTTTTCTTACAATCAGGTCTGCCGGCCCCTGTTTTAGCTGAAATATGGG
CTTTATCAGACCTAAACAAGGATGGGAAGATGGATCAGCAAGAGATCTCCATAGCTATGAAACTCATCAAACTGAAGCTT
CAAGGCCAACGGTTGCCTGTGGTTCTCCCTCCTATTATGAAGCAACCCCCTTTGTTTTCTCCATTAATTTCTGCTCGTTT
TGGAATGGGAAGCATGCCCAATCTGTCCATTCCTCAGTCATTGCCTCCAGCTGCACCTATAACATCACTGTCTTCTACAA
CTTCAGGGACCAGCCTTCCTCCCTTAATGATGCCCACTCCCCTTAGTACCTTCTGTTAGCACATCATCATTACCAAATGG
AACCACCAATCTCATTCAGCCTTTATCTATTCCTTATTCTTCTTCAACATTGCCTTATGGGTCATCTTATAGTCTGATGA
TGGGAGGATTTGGAGGTGCTAGTATACAGAAAGCCCAGTCTCTGATTGATTTAGGATCTAGTAGCTCAACTTCCTCGACT
GCTTCACTCTCAGGGAACTCACCCAAGACTGGGACCTCAGAGTGGGCAGTTCCTCAGCCTTCAAGATTAAAATATCAGCA
GAAATTCAGTAGTCTTGACAAAAGCATGAGTGGATATCTCTCAGGTTTTCAAGCTAGAAATGCCCTTCTTCAGTCAAATC
TTTCTCAAACTCAGCTAGCTACTATTTGGACTCTAGCTGACATCGATGGTGATGGACAGCTAAAAGCAGAAGAGTTTATC
CTTGCAATGCACCTCACTGACATGGCCAAAGCTGGACAGCCATTACCACTGACTTTACCGCCTGAGCTTGTCCCTCTGTC
TTTCAGAGGAGGAAAGCAAATTGATTCCATTAATGGAATTCTGCCTTCATATCAGAAAATGCAAGAAGAGGAACCTCAGA
AGAAATTACCAGTTACTTTTGAGGACAAACAGAAAGTCAACTATGAGCGAGGGAGCATGGAGCTGGAGAAGTGACACCAA
GATTTGATGGAGCAGCAGCAGAGGGAGGCAGAATGTAAAGCCCAGAAAGAAAAGAGTGGGAATGGAAACAGAGAGAATTA
CAAAAACAAGAACGGAAGAAACAATTTGAATTAGAAAAACGCTTGAAAAAGCAGCGGGAATTGGAGAGACAACGAGAGGA
AGAAAGGAGAAAAGAGATAGAAAGACAAGAAGCAGCAAAACAGGAACTTGAATGACAGTGTCGCTTAGAATGGGAGAGAA
TTTGACGACAGGAGCTTCTTAATCAAAAGAATAGAGAACAAGAAGAAATTGTCAGGTTAAACTCTAAAAAGAAGAGTCTT
CATCTTGAGTTGGAAGCACTGAATGGCAAACATCAGCAGATCTCAGGCAGACTTCAGGATGTCCGACTCAAAAAGCAAAC
TCAAAAGACTGAGCTGGAAGTTCTGGATAAGCAGTGTGACCTGGAAATTACGGAAATCAAGCAACTACTACAGGACTTCA
GGAATATCAGAATAAGCTTATCTATCTGGTACCTGAGAAGCAATTATTAAATGAAAGAATTAAAAACATGCAGTTCAGTA
ACACAGCTGATTCAGGGATCAGTTTACTTCATAAAAAATCATTAGAAAAGGAAGAATTATGCCAAAGACTTAAAGAACAA
TTAGATGCTCTTGAGAAAGAAACGGCATCTAAGCTATCAGAAATGGATTCTTTTAACAATGAGCTA

Alignment

ORF - retro_cjac_3080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.66 %
• Parental protein coverage: 51.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GGPNMWAITSEERTKHDRQFDNLKPSGGYITGDQARNFFLQSGLPAPVLAEIWALSDLNKDGKMDQQEFS
          GGPNMWAITSEE.TKHDRQFDNLKPSGGYITGDQA.NFFLQSGLPAPVLAEIWALSDLNKDGKMDQQE.S
Retrocopy GGPNMWAITSEESTKHDRQFDNLKPSGGYITGDQAHNFFLQSGLPAPVLAEIWALSDLNKDGKMDQQEIS

Parental  IAMKLIKLKLQGQQLPVVLPPIMKQPPLFSPLISARFGMGSMPNLSIPQPLPPAAPITSLSSATSGTSLP
          IAMKLIKLKLQGQ.LPVVLPPIMKQPPLFSPLISARFGMGSMPNLSIPQ.LPPAAPITSLSS.TSGTSLP
Retrocopy IAMKLIKLKLQGQRLPVVLPPIMKQPPLFSPLISARFGMGSMPNLSIPQSLPPAAPITSLSSTTSGTSLP

Parental  PLMMPTPL-VPSISTSSLPNGTASLIQPLSIPYSSSTLPHGSSYSLMMGGFGGASIQKAQSLIDLGSSSS
          PLMMPTPL.VPS.STSSLPNGT..LIQPLSIPYSSSTLP.GSSYSLMMGGFGGASIQKAQSLIDLGSSSS
Retrocopy PLMMPTPL>VPSVSTSSLPNGTTNLIQPLSIPYSSSTLPYGSSYSLMMGGFGGASIQKAQSLIDLGSSSS

Parental  TSSTASLSGNSPKTGTSEWAVPQPSRLKYRQKFNSLDKSMSGYLSGFQARNALLQSNLSQTQLATIWTLA
          TSSTASLSGNSPKTGTSEWAVPQPSRLKY.QKF.SLDKSMSGYLSGFQARNALLQSNLSQTQLATIWTLA
Retrocopy TSSTASLSGNSPKTGTSEWAVPQPSRLKYQQKFSSLDKSMSGYLSGFQARNALLQSNLSQTQLATIWTLA

Parental  DIDGDGQLKAEEFILAMHLTDMAKAGQPLPLTLPPELVPPSFRGGKQIDSINGTLPSYQKMQEEEPQKKL
          DIDGDGQLKAEEFILAMHLTDMAKAGQPLPLTLPPELVP.SFRGGKQIDSING.LPSYQKMQEEEPQKKL
Retrocopy DIDGDGQLKAEEFILAMHLTDMAKAGQPLPLTLPPELVPLSFRGGKQIDSINGILPSYQKMQEEEPQKKL

Parental  PVTFEDKRKANYERGNMELEKRRQALMEQQQR-EAERKAQKEKEEWERKQRELQEQEWKKQLELEKRLEK
          PVTFEDK.K.NYERG.MELEK..Q.LME.QQ..E..R....E..EWE.KQRELQ.QE.KKQ.ELEKRL.K
Retrocopy PVTFEDKQKVNYERGSMELEK*HQDLME-QQQ<EGGRM*SPERKEWEWKQRELQKQERKKQFELEKRLKK

Parental  QRELERQREEERRKEIERREAAKQELERQRRLEWERIRRQELLNQKNREQEEIVRLNSKKKSLHLELEAL
          QRELERQREEERRKEIER.EAAKQELE.Q.RLEWERI.RQELLNQKNREQEEIVRLNSKKKSLHLELEAL
Retrocopy QRELERQREEERRKEIERQEAAKQELE*QCRLEWERI*RQELLNQKNREQEEIVRLNSKKKSLHLELEAL

Parental  NGKHQQISGRLQDVRLKKQTQKTELEVLDKQCDLEITEIKQLLQE-LQEYQNKLIYLVPEKQLLNERIKN
          NGKHQQISGRLQDVRLKKQTQKTELEVLDKQCDLEITEIKQLLQ..LQEYQNKLIYLVPEKQLLNERIKN
Retrocopy NGKHQQISGRLQDVRLKKQTQKTELEVLDKQCDLEITEIKQLLQD<LQEYQNKLIYLVPEKQLLNERIKN

Parental  MQFSNTPDSGISLLHKKSLEKEELCQRLKEQLDALEKETASKLSEMDSFNNQL
          MQFSNT.DSGISLLHKKSLEKEELCQRLKEQLDALEKETASKLSEMDSFNN.L
Retrocopy MQFSNTADSGISLLHKKSLEKEELCQRLKEQLDALEKETASKLSEMDSFNNEL

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	0.04 RPM	48.99 RPM
SRP051959_heart	0.37 RPM	34.52 RPM
SRP051959_kidney	0.80 RPM	42.29 RPM
SRP051959_liver	0.06 RPM	24.87 RPM
SRP051959_lung	1.01 RPM	67.02 RPM
SRP051959_lymph_node	0.16 RPM	83.86 RPM
SRP051959_skeletal_muscle	0.11 RPM	18.56 RPM
SRP051959_spleen	0.21 RPM	67.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3080 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3080 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3080 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 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,