RetrogeneDB ID: retro_cjac_3278

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:20312285..20313021(-)
• Located in intron of: None

Retrocopy information

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

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_3278
GAGCCGGAGCCTGAGGCCGAGCCTGAAGAGGAGCCACCCCGACCCCGCGCTCCGCCCCAGGGAACTCCCGGCCCTGGGCC
TGGTTCGGGAGCCCCCGGTAGTCAAGAGGAGGAGGAGGAGGAGCCGGGACTGGTCGAGGGTGACCCGGGGGGACGGCACC
ATTGAGGACTGGGAGCTGGAAACTATCAAAGCTCGAGTCAGGGAGATGGCGGAAGAAGCTGAGAAGCTAAAGGAACTACA
GAACGAGGTAGAGAAGCAGATGAATATGAGTCCACCTCCAGGCAATGCTGGCCCAGTGATCATGTCCACTGAGGAGATGC
TAGAGGCTGATGCCCGTTCCATCTATGTCGGCAATGTGGACTATGGTACAACAGCAGAAGAGCTGGAAGCTCACTTTCAT
GGCGTGGCTCAGTCAACCGTGTTACCATACTCTGACAAATTTAGTGGCCATCCCAAAGGGTTTGCATATATAGAGTTCTC
AGATAAAGAGTCAGCGAGAACTTACTTGGCCTAGGATGAGTCCCTATTTAGAGGAAGGCAAATCAAGGTGATCCCAAAAC
GAACCAACAGACCCGGCATCAGCACAACAGATGGGGGTTTTCCACGAGCCCGCTACCGTGCGTGGACCACCGACTACAAC
AGTTCCCGCTCTCGATTCTACAGTGGTTTTAACAGCAGGCCCCGGGGGCGCGTCTACAGAGGCCAGGCTAGAGCCACATC
ATGGTATTTCCCTTAC

Alignment

ORF - retro_cjac_3278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.45 %
• Parental protein coverage: 79.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EPEPEPEPEEEPPRPRAPP-GAPGPGPGSGAPGSQEEEEE-PGLVEGDPG-DGAIEDPELEAIKARVREM
          EPEPE.EPEEEPPRPRAPP.G.PGPGPGSGAPGSQEEEEE.PGLVEGDPG.DG.IED.ELE.IKARVREM
Retrocopy EPEPEAEPEEEPPRPRAPPQGTPGPGPGSGAPGSQEEEEEEPGLVEGDPG>DGTIEDWELETIKARVREM

Parental  EEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVN
          .EEAEKLKELQNEVEKQMNMSPPPGNAGPVIMS.EE..EADARSIYVGNVDYG.TAEELEAHFHG.....
Retrocopy AEEAEKLKELQNEVEKQMNMSPPPGNAGPVIMSTEEMLEADARSIYVGNVDYGTTAEELEAHFHGVAQ-S

Parental  RVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTDRGFPRARYRAR
          .V....DKFSGHPKGFAYIEFSDKES.RT.LA.DESLFRGRQIKVIPKRTNRPGISTTD.GFPRARYRA.
Retrocopy TVLPYSDKFSGHPKGFAYIEFSDKESARTYLA*DESLFRGRQIKVIPKRTNRPGISTTDGGFPRARYRAW

Parental  TTNYNSSRSRFYSGFNSRPRGRVYRGRARATSWYSPY
          TT.YNSSRSRFYSGFNSRPRGRVYRG.ARATSWY.PY
Retrocopy TTDYNSSRSRFYSGFNSRPRGRVYRGQARATSWYFPY

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	16.84 RPM
SRP051959_heart	0.00 RPM	32.03 RPM
SRP051959_kidney	0.00 RPM	56.46 RPM
SRP051959_liver	0.00 RPM	25.93 RPM
SRP051959_lung	0.03 RPM	38.26 RPM
SRP051959_lymph_node	0.00 RPM	38.42 RPM
SRP051959_skeletal_muscle	0.00 RPM	20.05 RPM
SRP051959_spleen	0.00 RPM	36.64 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3278 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3278 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3278 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,