RetrogeneDB ID: retro_pabe_3755

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:50025520..50025944(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPB1
• Ensembl ID: ENSPPYG00000029733
• Aliases: None
• Description: heat shock 27kDa protein 1 [Source:HGNC Symbol;Acc:5246]

Sequence

>retro_pabe_3755
CCTTCGGGCTGGTCGCAGTGGTTCGGCACCAGCGGCTGGCCCGGCTACGTGCGCCCCCTCCCCCCGCCGCGGTCTAGAGC
CCCGCGGTGGCCGCGCCCGCCTACAGCCACGCGCTCAGCCGGCAGCTCAGTAGCGGGGTCTCGGAGAACCGGCCCACAGC
GGACCTCTGGCGAGTATCCCTGGACATCAACCACTTCGCCTCCGACGAGCTGACGGTCAAGACCAAGGATGGCATGGTGG
AGATCACCGGCAAGCACGAGCAGCGGCAGGACGAGCGTGGCTCCATCTCCAGATGCTTTACCCGGAAATACACGCTGCCC
CCCGGTGTGGACCCCACCAAGGTCTCCTCCTCCCTGTCCCCTGAGGGCACACTGACCGTGGAGGCCCCCATGCCCAAGCT
AGCCACGCAGTCCAACGAGATCAC

Alignment

ORF - retro_pabe_3755 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.42 %
• Parental protein coverage: 67.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PEEWSQWFGGSSWPGYVRPLPP-AAIESPAVAAPAYSRALSRQLSSGVSEIRHTADRWRVSLDVNHFAPD
          P..WSQWFG.S.WPGYVRPLPP.AA..SPAVAAPAYS.ALSRQLSSGVSE.R.TAD.WRVSLD.NHFA.D
Retrocopy PSGWSQWFGTSGWPGYVRPLPP<AAV*SPAVAAPAYSHALSRQLSSGVSENRPTADLWRVSLDINHFASD

Parental  ELTVKTKDGVVEITGKHEERQDEHGYISRCFTRKYTLPPGVDPAQVSSSLSPEGTLTVEAPMPK-GSHAV
          ELTVKTKDG.VEITGKHE.RQDE.G.ISRCFTRKYTLPPGVDP..VSSSLSPEGTLTVEAPMPK..SHAV
Retrocopy ELTVKTKDGMVEITGKHEQRQDERGSISRCFTRKYTLPPGVDPTKVSSSLSPEGTLTVEAPMPK<ASHAV

Parental  QRDH
          QRDH
Retrocopy QRDH

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	13.99 RPM	66.96 RPM
SRP007412_cerebellum	1.58 RPM	11.92 RPM
SRP007412_heart	26.13 RPM	124.60 RPM
SRP007412_kidney	66.96 RPM	275.75 RPM
SRP007412_liver	21.82 RPM	126.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3755 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3755 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3755 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4830
Gorilla gorilla	retro_ggor_3012

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016303	5 retrocopies	retro_cjac_1914, retro_cjac_2499, retro_cjac_396, retro_cjac_412, retro_cjac_591,
Homo sapiens	ENSG00000106211	1 retrocopy	retro_hsap_4830,
Gorilla gorilla	ENSGGOG00000002700	1 retrocopy	retro_ggor_3012,
Mus musculus	ENSMUSG00000004951	1 retrocopy	retro_mmus_1097,
Pongo abelii	ENSPPYG00000029733	1 retrocopy	retro_pabe_3755 ,