RetrogeneDB ID: retro_cjac_1263

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:16643051..16643830(-)
• Located in intron of: ENSCJAG00000016540

Retrocopy information

• Ensembl ID: ENSCJAG00000016558
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PABPN1
• Ensembl ID: ENSCJAG00000007960
• Aliases: None
• Description: poly(A) binding protein, nuclear 1 [Source:HGNC Symbol;Acc:8565]

Sequence

>retro_cjac_1263
GGGGGCGCAGGGGACTACGGGAACGGGAACGGCCTGGAGTCTGGGGAACTGGAGCCTGAGGAGCTGCTGCCGGAGCCCGA
GCCGGAGCCCGCCCTTGAAGAGGAACCGCCCCGGCCCCACGCCCCACGCCCCCAGGAGCTCCGGGCCATGGGCATGGATC
GGGAGACCCCGGCAGCCAAGAGAAGGAGGAGGAGCCGGGACTGGTCGAGGGTGACCCGGAGCTGGAAGCTATCAAAGCTG
GAGTCAGGGAGATGGAGGAAGAAGCTGAGAAGCGAAAGGAACTACAGAACGAGGTAGAGAAGCAGATGAATATGAGTCCA
CCTCCAGGCAATGCTGGCCCAGTGATCATGCCCATTGAGGAGAAGATGGAGGCTGATGCCCGTTCCATCTATGTTGGCAG
TGTGGACTTGGTGCAACAGCAGAAGAGCTGGAAGCTCACTTTCATGGCTGTGGTTCAGTCAACCGTGTTACCATACTCTG
TGACAAATTTAGCGGCCATCCCAAAGGGTTTGCATATGTAAGAGTTCTCAGAGAAAGAGTTAGTGAGGACTTCCTTGGCT
TTAGATGAGTCCCTATTTAGAGGAAGGCAAATCAAGGTGATCCCAAAACGAACCAACAGACCAGGCATCAGTACAGCAGA
CCCGGGTTTTCCACGAGTCCACTACCGCGCACGGACCACCAACTACAACAGCTCACCCTCTCGATTCTACAGTGGTTTTA
ACAGCAGGCCCCGGGGTCGCGCCTACAGGGGCCGGGCTAGAGTGACATCGTGGTATTCC

Alignment

ORF - retro_cjac_1263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.99 %
• Parental protein coverage: 96.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GRGGDYGNG--LESEELEPEELLLEPEPEP-EPEEG-APGPGPGS-GAPGSQEEEEEPGLVEGDPGDGAI
          G..GDYGNG..LES.ELEPEELL.EPEPEP..P..G.AP.P.P...GAPG.......PG..E.....G..
Retrocopy GGAGDYGNGNGLESGELEPEELLPEPEPEP<RP*RGTAPAPRPTPPGAPGHGHGSGDPGSQEKEEEPGLV

Parental  E-DPELEAIKARVREMEEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSIEEKMEADARSIYVGNVD-YG
          E.DPELEAIKA.VREMEEEAEK.KELQNEVEKQMNMSPPPGNAGPVIM.IEEKMEADARSIYVG.VD..G
Retrocopy EGDPELEAIKAGVREMEEEAEKRKELQNEVEKQMNMSPPPGNAGPVIMPIEEKMEADARSIYVGSVD<LG

Parental  ATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYI-EFSDKESVRTSLALDESLFRGRQIKVIPKRTNR
          ATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAY..EFS.KE.VRTSLALDESLFRGRQIKVIPKRTNR
Retrocopy ATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYV>EFSEKELVRTSLALDESLFRGRQIKVIPKRTNR

Parental  PGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNSRPRGRVYRGRARATSWYS
          PGIST.D.GFPR..YRARTTNYNSS.SRFYSGFNSRPRGR.YRGRAR.TSWYS
Retrocopy PGISTADPGFPRVHYRARTTNYNSSPSRFYSGFNSRPRGRAYRGRARVTSWYS

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	16.84 RPM
SRP051959_heart	0.11 RPM	32.03 RPM
SRP051959_kidney	0.47 RPM	56.46 RPM
SRP051959_liver	0.13 RPM	25.93 RPM
SRP051959_lung	0.18 RPM	38.26 RPM
SRP051959_lymph_node	0.16 RPM	38.42 RPM
SRP051959_skeletal_muscle	0.11 RPM	20.05 RPM
SRP051959_spleen	0.84 RPM	36.64 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1263 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1263 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1263 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006884	1 retrocopy	retro_btau_693,
Callithrix jacchus	ENSCJAG00000007960	4 retrocopies	retro_cjac_1263 , retro_cjac_2291, retro_cjac_3278, retro_cjac_3836,
Dipodomys ordii	ENSDORG00000002873	1 retrocopy	retro_dord_606,
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Gorilla gorilla	ENSGGOG00000022683	2 retrocopies	retro_ggor_1454, retro_ggor_3030,
Mustela putorius furo	ENSMPUG00000006775	1 retrocopy	retro_mputfur_496,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403,
Nomascus leucogenys	ENSNLEG00000015009	2 retrocopies	retro_nleu_2066, retro_nleu_3023,
Otolemur garnettii	ENSOGAG00000008710	1 retrocopy	retro_ogar_797,
Pongo abelii	ENSPPYG00000005663	2 retrocopies	retro_pabe_1645, retro_pabe_3773,
Pan troglodytes	ENSPTRG00000006168	2 retrocopies	retro_ptro_1339, retro_ptro_3232,
Sus scrofa	ENSSSCG00000002023	1 retrocopy	retro_sscr_625,