RetrogeneDB ID: retro_cjac_3950

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286383.1:4055..5701(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000020322
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MATR3
• Ensembl ID: ENSCJAG00000006888
• Aliases: None
• Description: matrin-3 [Source:RefSeq peptide;Acc:NP_001192169]

Sequence

>retro_cjac_3950
CCTCTCCCTTTCCCTAAGGAGTGGAGTCAACATATCAATGGAGCAAGTCACAGTCGTCGATGCCAGCTTCTTCTTGAAAT
CTACCCAGAATGGAATCCTGACAATGATACAGGACATACAATGGGTGATCCATTCATGTTGCAGCAGTCTACAAATCCAG
CACCAGGAATTCTGGGACCTCCACCTCCCTCGTTTCATCTTGGGGGACCAGCAGTTGGGCCAAGAGGAAATCTGGGTGCT
GGAAATGGAAACCTGCAGGGACCTAGACACATGCAAAAAGGCAGAGTGGAAACTAGCAGAGTTGTTCACATCATGGATTT
TCAACGAGGGAAAAACTTGAGATATCAGCTGTTACAACTGGTGGAACCATTTGGAGTCATTTCAAATCATCTGATTCTAA
ATAAAATTAATGAGGCATTTATTGAAATGGCAACCACAGAGGATGCTCAGGCCGCGGTGGATTATTATACAACCACACCA
GCGTTAGTATTTGGCAAGCCAGTGAGAGTTCATTTATCCCAGAAGTATAAAAGAATAAAGAAACCTGAAGGAAAGCCAGA
TCAGAAGTTTGATCAAAAGCAAGAGCTTGGACGTGTGATACACTCAGCAATTTGCCTCATTCTGGCTATTCTGACAGTGC
TGTCCTCAAGCTTGCTGAGCCCTATGGGAAAATAAAGAATTACATATTGATGAGGATGAAAAGTCAGGCTTTTATTGAGA
TGGAGACAAGAGAAGATGCAATGGCAATGGTTGACCATTGTTTGAAAAAAGCTCTTTGGTTTCAGGGGAGATGTGTGAAG
GTTGACCTGTCTGAGAAATATAAAAAACTGGTACTGAGGATTCCCAACAGAGGCATTGATTTACTGAAAAAAGATAAATC
CCGGAAAAGATCTTATTCTCCAGACGGCAAAGAATCTCCAAGTGATAAGAAATCTAAGACTGATGGTTCCCAGAAGACTG
AAAGTTCAACCGAAGGTAAAGAACAAGAAGAGAAGTCCGGTGACGATGGTGAGAAAGACACAAAGGATGACCAGACAGAG
CAGGAACCTAATATGCTTCTTGAATCTGAAGATGAACTACTTGTCGATGAAGAAGAAGCAGCAGCACTGCTAGAAAGTGG
CAGTTCAGTGGGAGACGAGGCCGATCTTGCTAATTTAGGTGATGTGACTTCTGATGGAAAAAAGGAATCTTCAGAAAAAG
CTGTGAAAAAAGATGCAAGTGCTTCAGCAGCAGCAAAGAAAAAGCTTAAAAAGGTGGACAAGATCGAGGAACTTGATCAA
GAAAATGAAGCAGCGTTGGAAAATGGAATTAAAAATGAGGAAAATACAGAACCAGGTGCTGAATCTGCTGAGAACGCTGA
AGATCCCAACAAAGATACAAGTGAAAATGCAGATGGTCAAAGTGATGAGAACAAGGAGGACTATACAATCCCAGATGAGT
ATAGAATTGGACCGTATCAGCCCAACGTTCCTGTTGGTATAGACTATGTGATACCTAAAACAGGGTTTTACTGTAAGCTG
TGTTCACTCTTTTATACAAATGAAGAAGTTGCAAAGAATACTCACTGCAGCAGCCTTCCTCATTATCAGAAATTAAAGAA
ATTTCTGAATAAATTGGCAGAAGAACGCAGGCAGAAGAAGGAAACT

Alignment

ORF - retro_cjac_3950 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.09 %
• Parental protein coverage: 64.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PVHSNKEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQQSTNPAPGILGPPPPSFHLGGP
          P....KEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQQSTNPAPGILGPPPPSFHLGGP
Retrocopy PLPFPKEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQQSTNPAPGILGPPPPSFHLGGP

Parental  AVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAF
          AVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAF
Retrocopy AVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAF

Parental  IEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFDQKQELGRVIH-LSNLPHSG
          IEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFDQKQELGRVIH.LSNLPHSG
Retrocopy IEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFDQKQELGRVIH<LSNLPHSG

Parental  YSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVL
          YSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVL
Retrocopy YSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVL

Parental  RIPNRGIDLLKKDKSRKRSYSPDGKESPSDKKSKTDGSQKTESSTEGKEQEEKSGDDGEKDTKDDQTEQE
          RIPNRGIDLLKKDKSRKRSYSPDGKESPSDKKSKTDGSQKTESSTEGKEQEEKSGDDGEKDTKDDQTEQE
Retrocopy RIPNRGIDLLKKDKSRKRSYSPDGKESPSDKKSKTDGSQKTESSTEGKEQEEKSGDDGEKDTKDDQTEQE

Parental  PNMLLESEDELLVDEEEAAALLESGSSVGDEADLANLGDVTSDGKKESSEKAVKKDASASAAAKKKLKKV
          PNMLLESEDELLVDEEEAAALLESGSSVGDEADLANLGDVTSDGKKESSEKAVKKDASASAAAKKKLKKV
Retrocopy PNMLLESEDELLVDEEEAAALLESGSSVGDEADLANLGDVTSDGKKESSEKAVKKDASASAAAKKKLKKV

Parental  DKIEELDQENEAALENGIKNEENTEPGAESAENAEDPNKDTSENADGQSDENKEDYTIPDEYRIGPYQPN
          DKIEELDQENEAALENGIKNEENTEPGAESAENAEDPNKDTSENADGQSDENKEDYTIPDEYRIGPYQPN
Retrocopy DKIEELDQENEAALENGIKNEENTEPGAESAENAEDPNKDTSENADGQSDENKEDYTIPDEYRIGPYQPN

Parental  VPVGIDYVIPKTGFYCKLCSLFYTNEEVAKNTHCSSLPHYQKLKKFLNKLAEERRQKKET
          VPVGIDYVIPKTGFYCKLCSLFYTNEEVAKNTHCSSLPHYQKLKKFLNKLAEERRQKKET
Retrocopy VPVGIDYVIPKTGFYCKLCSLFYTNEEVAKNTHCSSLPHYQKLKKFLNKLAEERRQKKET

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	0.13 RPM	78.41 RPM
SRP051959_heart	0.21 RPM	113.27 RPM
SRP051959_kidney	0.20 RPM	125.11 RPM
SRP051959_liver	0.37 RPM	95.67 RPM
SRP051959_lung	0.44 RPM	118.70 RPM
SRP051959_lymph_node	0.66 RPM	145.20 RPM
SRP051959_skeletal_muscle	0.07 RPM	88.90 RPM
SRP051959_spleen	0.63 RPM	136.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3950 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3950 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3950 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006888	1 retrocopy	retro_cjac_3950 ,
Homo sapiens	ENSG00000015479	1 retrocopy	retro_hsap_199,
Gorilla gorilla	ENSGGOG00000007308	2 retrocopies	retro_ggor_276, retro_ggor_421,
Nomascus leucogenys	ENSNLEG00000009093	1 retrocopy	retro_nleu_1849,
Oryctolagus cuniculus	ENSOCUG00000026311	1 retrocopy	retro_ocun_652,
Otolemur garnettii	ENSOGAG00000010607	1 retrocopy	retro_ogar_3417,
Pongo abelii	ENSPPYG00000015835	2 retrocopies	retro_pabe_1722, retro_pabe_438,
Pan troglodytes	ENSPTRG00000017294	1 retrocopy	retro_ptro_181,
Rattus norvegicus	ENSRNOG00000019875	2 retrocopies	retro_rnor_1124, retro_rnor_475,