RetrogeneDB ID: retro_ptro_464

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:123484742..123485306(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX2
• Ensembl ID: ENSPTRG00000008673
• Aliases: None
• Description: Y box binding protein 2 [Source:HGNC Symbol;Acc:17948]

Sequence

>retro_ptro_464
GTCTTTGTTCACTAGACAGCTGTTAAAAGAAACAACCCCAGGAAGTTTCTGCGCAGCGTTAGAGATGGGGAGACTGTGGA
ATTTGATGTCGTGGAAGGAGAGAAGGGCGCAGAAGCCACTAATGTAACTGGGCCCAGGGCGGGGGTGCCCATGAAGGGCA
CCGTTATGCCCCCAACTGACGTAGGTTCCGCTGATTCATCCCCGGCCTCCCTCAGTTGCCCCACCACCCATGGTGGCAGA
GATCCCCTCTCGGGGGACAGAACCTGGCGGCGAAGGGGAGCGGGCCGAAGACTCTGGGCAGCGGCCCAGACGATGGCGCC
CCCCACCCTTCTACCTACGGCGGTTTGTGCGAGGCCCCCGGCCCCCCAACCAGCAGCAGCCTATAGAGGGCACTGATGGG
GTAGAACCAAACAGACAGCCCCATTGGAGGGGCACCAACAGCAGGGAGATGAGTGGGTCCCCCCGCCCAGATTCCGGCCC
AGGTACCTAAGGCCTTTACACCCCAGGCCACCCCAGCAGCCTACCATGGAAGGTGGGGACAGTGATACCAAGCCCAGCCA
AGGA

Alignment

ORF - retro_ptro_464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.94 %
• Parental protein coverage: 51.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VFVHQTAIKRNNPRKFLRSVGDGETVEFDVVEGEKGAEATNVTGP-GGVPVKGS-RYAPNRRKSRRFIP-
          VFVH.TA.KRNNPRKFLRSV.DGETVEFDVVEGEKGAEATNVTGP..GVP.KG..RYAPN.R..R.FIP.
Retrocopy VFVH*TAVKRNNPRKFLRSVRDGETVEFDVVEGEKGAEATNVTGPRAGVPMKGT<RYAPN*RRFR*FIP<

Parental  RPPSVAPPPMVAEIPSAGTGPGSKGERAEDSGQRPRRWCPPPFFYRRRFVRGPRPPNQQQPIEGTDRVEP
          RPPSVAPPPMVAEIPS.GT.PG..GERAEDSGQRPRRW.PPPF.Y.RRFVRGPRPPNQQQPIEGTD.VEP
Retrocopy RPPSVAPPPMVAEIPSRGTEPGGEGERAEDSGQRPRRWRPPPF-YLRRFVRGPRPPNQQQPIEGTDGVEP

Parental  -KETAPLEGHQQQGDERVPPPRFRPRYRRPFRPRPRQQPTTEGGDGETKPSQG
          .K.TAPLEGHQQQGDE.VPPPRFRPRY.RP..PRP.QQPT.EGGD..TKPSQG
Retrocopy <KQTAPLEGHQQQGDEWVPPPRFRPRYLRPLHPRPPQQPTMEGGDSDTKPSQG

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.43 RPM
SRP007412_cerebellum	0.00 RPM	0.11 RPM
SRP007412_heart	0.00 RPM	0.52 RPM
SRP007412_kidney	0.00 RPM	1.39 RPM
SRP007412_liver	0.00 RPM	1.60 RPM
SRP007412_testis	0.84 RPM	144.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_464 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_464 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_464 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_637

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016581	1 retrocopy	retro_cjac_1473,
Homo sapiens	ENSG00000006047	1 retrocopy	retro_hsap_637,
Macaca mulatta	ENSMMUG00000022712	1 retrocopy	retro_mmul_2237,
Nomascus leucogenys	ENSNLEG00000008063	1 retrocopy	retro_nleu_1954,
Oryctolagus cuniculus	ENSOCUG00000015064	1 retrocopy	retro_ocun_1762,
Pan troglodytes	ENSPTRG00000008673	3 retrocopies	retro_ptro_1264, retro_ptro_464 , retro_ptro_50,