RetrogeneDB ID: retro_ptro_50

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:224655426..224656398(-)
• Located in intron of: ENSPTRG00000002185

Retrocopy information

• Ensembl ID: ENSPTRG00000006456
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

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_50
ATGAGCAGCGAGGCCGAGACCCAGCAGCCGCCCGCCGCCCCCCCCGCCGCCCCCGCCCTCAGCGCCGCCGACACCAAGCC
CGGCACTACGGGCAGCGGCGCAGGGAGCGGTGGCCCGGGCGGCCTCACATCGGCGGCGCCTGCCGGCGGGGACAAGAAGG
TCATCGCAACGAAGGTTTTGGGAACAGTAAAATGGTTCAATGTAAGGAACGGATATGGTTTCATCAACAGGAATGACACC
AAGGAAGATGTATTTGTACACCAGACTGCCATAAAGAAGAAGAACCCCAGGAAGTACCTTCGCAGTGTAGGAGATAGAGA
GACTGTGGAGTTTGATGTTGTTGAAGGAGAAAAGGGTGCGGAGGCAGCAAATGTTACAGGTCCTGGTGGTGTTCCAGTTC
AAGGCAGTAAATATGCAGCAGACCGTAACCATTATAGACGCTATCCACGTCGTAGGGGTCCTCCACGCAATTACCAGCAA
AATTACCAGAACAGTGAGAGTGGGGAAAAGAACGAGGGATCGGAGAGTGCTCCCGAAGGCCAGGCCCAACAACGCCGGCC
CTACCGCAGGCGAAGGTTCCCACCTTACTACATGCGGAGACCCTATGGGCGTCGACCACAGTGTTCCAACCCTCCTGTGC
AGGGAGAAGTGATGGAGGGTGCTGACAACCAGGGTGCAGGAGAACAAGGTAGACCAGTGAGGCAGAATATGTATCGGGGA
TATAGACCACGATTCCGCAGGGGCCCTCCACGCCAAAGACAGCCTAGAGAGGACGGCAATGAAGAAGATAAAGAAAATCA
AGGAGATGAGACCCAAGGTCAGCAGCCACCTCAACGTCGGTACCGCCGCAACTTCAATTACCGACGCAGACGCCCAGAAA
ACCCTAAACCACAAGATGGCAAAGAGACAAAAGCAGCCGATCCACCAGCTGAGAATTCGTCCGCTCCCGAGGCTGAGCAG
GGCGGGACTGAG

Alignment

ORF - retro_ptro_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.79 %
• Parental protein coverage: 50.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASGPATGTPSAPGPRTPGNPATAASGTPA---PPARSQADKPVLAIQVLGTVKWFNVRNGYGFINRNDTK
          A..PA....SA...........A.SG.P......A....DK.V.A..VLGTVKWFNVRNGYGFINRNDTK
Retrocopy AAPPAAPALSAADTKPGTTGSGAGSGGPGGLTSAAPAGGDKKVIATKVLGTVKWFNVRNGYGFINRNDTK

Parental  EDVFVHQTAIKRNNPRKFLRSVGDGETVEFDVVEGEKGAEATNVTGPGGVPVKGSRYAPNRRKSRRFIPR
          EDVFVHQTAIK..NPRK.LRSVGD.ETVEFDVVEGEKGAEA.NVTGPGGVPV.GS.YA..R...RR....
Retrocopy EDVFVHQTAIKKKNPRKYLRSVGDRETVEFDVVEGEKGAEAANVTGPGGVPVQGSKYAADRNHYRRY---

Parental  PPSVAPPPMVAEIPSAGTGPGSKGERAEDSGQRPRRWCPPPFFYRRRF
          .P....PP............G.K.E..E...........P....RRRF
Retrocopy -PRRRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRP--YRRRRF

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	3.15 RPM	0.43 RPM
SRP007412_cerebellum	2.76 RPM	0.11 RPM
SRP007412_heart	9.73 RPM	0.52 RPM
SRP007412_kidney	2.17 RPM	1.39 RPM
SRP007412_liver	4.45 RPM	1.60 RPM
SRP007412_testis	62.28 RPM	144.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_50 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_50 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_50 has 0 orthologous retrocopies within eutheria group .

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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 ,