RetrogeneDB ID: retro_cjac_4108

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:101360739..101362044(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023432
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTPN1
• Ensembl ID: ENSCJAG00000000531
• Aliases: None
• Description: None

Sequence

>retro_cjac_4108
ATGGAGATGGAAAAGGAGTTCGAGCAGATTGACAAGTCCAGGAGCTGGGAGGCCATTTACCAGGATATCGAACACAAAAC
CAGTGACTTCCCGTGTAGAGTGGCTGAGCTTCCTAAGAACAAAAACCGAAATAGGTATAGAGATGTCAGTCCCTTTGACC
ATAGTCGGATTAAACTACATCAAGAAGATAACGACTATATCAATGCCAGTTTGATAAAAATGGAAGAAGCCCAAAGGAGT
TACATTCTTACCCAGGGCCCTTTGCCTAACACGTGCGGGCACTTTTGGGAGATGGTGTGGGAGCAGAAGAGCAGGGGTGT
CGTCATGCTCAGCAGAGTGATGGAGAAAGGCTCGTTAAAATGCGCACAGTACTGGCCACAAAAAGAAGAAAAAGAAATGA
TCTTTGAAGACACAAATTTGAAAATAACATTGATCTCTGAAGATAACAAGTCATATTATACAATTGGACAGCTAGAACTG
GAAAACCTTACAACCCAAGAAACTCGAGAGATCTTACATTTCCACTATACCACATGGCCTGACTTTGGAGTCCCGGAATC
GCCAGCCTCATTCTTGAACTTTCTTTTCAAAGTCCGAGAGTCGGGGTCACTCAGTCTGGAGCACGGCCCTGTGGTGGTGC
ACTGCAGTGCGGGCATTGGCAGGTCTGGGACCTTCTGTCTGGCTGATACCTGCCTCATGCTGATGGACAAAAGGAAAGAC
CCTTCATCCGTTGATATCAAGAAAGTACTGTTAGAAATGAGGAAGTTTCGGATGGGGCTGATCCAGACAGCAGACCAGCT
GCGCTTCTCCTACCTGGCTGTGATCGAAGGTGCCAAATTCATCATGGGAGACTCTTCCATGCAGGATCAGTGGAAGGAGC
TTTCCCACGAGGACCTGGAGCCCCTACCAGAGCACGTCCCCCGTTCTCCCTGGCCACCGAAAAGAATCCTGGAGCCACAC
AGTGGGAAATGCAGGGAGTTCTTCCCAAACCACCAGTGGGTGAAGGATGAGACTGGGGAGGATAAAGACTACCAGGTCAA
GGAAGAAACAGAAAGCCCCTTAAATGCCGCATCCTACAGCATGGAAAGCATAAGTCAAGAAACTGAAGTAAGAAGTCGGG
TCATGGGGGGAAGTCTTCGAGATGCCCAGGCTGCCTCCCCAGCCAAAGGGGAGCCGTCATCATCCGAGAAGGAGGAGGAC
CATGCACTGACTCACTGGAAGCCCTTCCTGGTCAACATGTGTGTGGCTGTGATCCTCACGGTTGGTGCATACCTGTGCTA
CAGGTTCCTGTTCAACAGCAACACA

Alignment

ORF - retro_cjac_4108 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.34 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINAS
          MEMEKEFEQIDKS.SW.AIYQDI.H..SDFPCRVA.LPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINAS
Retrocopy MEMEKEFEQIDKSRSWEAIYQDIEHKTSDFPCRVAELPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINAS

Parental  LIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNL
          LIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVML.RVMEKGSLKCAQYWPQKEEKEMIFEDTNL
Retrocopy LIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLSRVMEKGSLKCAQYWPQKEEKEMIFEDTNL

Parental  KLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGP
          K.TLISED.KSYYT..QLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLS.EHGP
Retrocopy KITLISEDNKSYYTIGQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSLEHGP

Parental  VVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKF
          VVVHCSAGIGRSGTFCLADTCL.LMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKF
Retrocopy VVVHCSAGIGRSGTFCLADTCLMLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKF

Parental  IMGDSSVQDQWKELSHEDVEPPPEHVPPPPRPPKRILEPHNGKCREFFPNHQWVKDETGEDKACPVKEET
          IMGDSS.QDQWKELSHED.EP.PEHVP..P.PPKRILEPH.GKCREFFPNHQWVKDETGEDK...VKEET
Retrocopy IMGDSSMQDQWKELSHEDLEPLPEHVPRSPWPPKRILEPHSGKCREFFPNHQWVKDETGEDKDYQVKEET

Parental  GSPLNATPYSMESMSQDTEVRSRVVGGSLRGAQAAFPAQGEPSPPKEEEDHALTHWKPFLVNMCLATVLM
          .SPLNA..YSMES.SQ.TEVRSRV.GGSLR.AQAA.PA.GEPS....EEDHALTHWKPFLVNMC.A..L.
Retrocopy ESPLNAASYSMESISQETEVRSRVMGGSLRDAQAASPAKGEPSSSEKEEDHALTHWKPFLVNMCVAVILT

Parental  ACAYLCYRFLFNSNT
          ..AYLCYRFLFNSNT
Retrocopy VGAYLCYRFLFNSNT

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	25.85 RPM
SRP051959_heart	0.02 RPM	16.38 RPM
SRP051959_kidney	0.02 RPM	16.26 RPM
SRP051959_liver	0.00 RPM	17.13 RPM
SRP051959_lung	0.00 RPM	43.21 RPM
SRP051959_lymph_node	0.00 RPM	44.61 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.89 RPM
SRP051959_spleen	0.06 RPM	69.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4108 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4108 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000531	1 retrocopy	retro_cjac_4108 ,
Callithrix jacchus	ENSCJAG00000005102	1 retrocopy	retro_cjac_1577,
Callithrix jacchus	ENSCJAG00000012464	1 retrocopy	retro_cjac_1051,
Ictidomys tridecemlineatus	ENSSTOG00000025542	1 retrocopy	retro_itri_17,