RetrogeneDB ID: retro_ptro_1264

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:43431639..43432359(+)
• 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_1264
GCTATTAAAAGAAACAACCCCAGGAAGTTTCTGCGCACCGTTGGAGATGGGGAGACTGTGGAATTTGATGTCGTGGAAGG
AGAGAAGGGCGCAGAAGCCACTAATGTAACTGGGCCCGGGGGAGTACCCGTGAAGGGCAGCCGTTATGCCCCCAACCGAC
GTAAGTCCCGCCGATTCATCCCCCGGCCTCCCTCAGTTGCCCCACCACCCATGGTGGCAGAGATCCCCTCGGCGGGGACA
GGACCTGGCAGTAAAGGGGAGCGGGCTGAAGACTCTGGGCAACGGCCCAGACGATGGTGCCCCCCACCCTTCTTCTACCG
ACGGCGGTTTGTGCGAGGCCCCCGGCCTCCCAACCAGCAGCAGCCTATAGAGGGCACTGACAGGGTAGAACCCAAAGAGA
CAGCCCCATTGGAGGGGCACCAACAGCAGGGAGATGAGCGGGTCCCCCCTCCCAGATTCCGGCCCAGGTACCGAAGGCCT
TTCCGCCCCAGGCCACGCCAGCAGCCTACCACAGAAGGTGGGGATGGTGAGACCAAGCCCAGCCAAGGTCCCGCTGATGG
TTCCCGGCCTGAGCCCCAGCGCCCACGAAACCGCCCCTACTTCCAGCGGAGACGGCAGCAGGCCCCTGGCCCCCAGCAGG
CCCCTGGCCCCCGGCAGCCCGCAGCCCCTGAGACCTCAGCCCCTGTCAACAGTGGGGACCCCACCACCACCATCCTGGAG

Alignment

ORF - retro_ptro_1264 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.25 %
• Parental protein coverage: 65.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AIKRNNPRKFLRSVGDGETVEFDVVEGEKGAEATNVTGPGGVPVKGSRYAPNRRKSRRFIPRPPSVAPPP
          AIKRNNPRKFLR.VGDGETVEFDVVEGEKGAEATNVTGPGGVPVKGSRYAPNRRKSRRFIPRPPSVAPPP
Retrocopy AIKRNNPRKFLRTVGDGETVEFDVVEGEKGAEATNVTGPGGVPVKGSRYAPNRRKSRRFIPRPPSVAPPP

Parental  MVAEIPSAGTGPGSKGERAEDSGQRPRRWCPPPFFYRRRFVRGPRPPNQQQPIEGTDRVEPKETAPLEGH
          MVAEIPSAGTGPGSKGERAEDSGQRPRRWCPPPFFYRRRFVRGPRPPNQQQPIEGTDRVEPKETAPLEGH
Retrocopy MVAEIPSAGTGPGSKGERAEDSGQRPRRWCPPPFFYRRRFVRGPRPPNQQQPIEGTDRVEPKETAPLEGH

Parental  QQQGDERVPPPRFRPRYRRPFRPRPRQQPTTEGGDGETKPSQGPADGSRPEPQRPRNRPYFQRRRQQAPG
          QQQGDERVPPPRFRPRYRRPFRPRPRQQPTTEGGDGETKPSQGPADGSRPEPQRPRNRPYFQRR......
Retrocopy QQQGDERVPPPRFRPRYRRPFRPRPRQQPTTEGGDGETKPSQGPADGSRPEPQRPRNRPYFQRRXXXXXX

Parental  PQQAPGPRQPAAPETSAPVNSGDPTTTILE
          ..............TSAPVNSGDPTTTILE
Retrocopy XXXXXXXXXXXXXXTSAPVNSGDPTTTILE

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	0.14 RPM	0.43 RPM
SRP007412_cerebellum	0.00 RPM	0.11 RPM
SRP007412_heart	0.03 RPM	0.52 RPM
SRP007412_kidney	0.08 RPM	1.39 RPM
SRP007412_liver	0.07 RPM	1.60 RPM
SRP007412_testis	17.28 RPM	144.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1264 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1264 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1264 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,