RetrogeneDB ID: retro_pabe_2705

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:173849915..173850842(+)
• Located in intron of: ENSPPYG00000016035

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP12
• Ensembl ID: ENSPPYG00000005232
• Aliases: None
• Description: ubiquitin specific peptidase 12 [Source:HGNC Symbol;Acc:20485]

Sequence

>retro_pabe_2705
ATGTAAATCCTAATGACAGTCTCCAAATTCGCTTCCATCTGTACCATGGGCGCCAATGCTTCGGCATTAGAGAAAGAGAT
TGGTCCAGAACAGTTTCCAGTGAATGAGCACTATTTTGGATTAGTCAGTTTTGGGAATACCTGCTACTGCAATTCAGTTC
TTCAAGCACTTTATTTTTGTCGTCCATTTCGGGAAACAGTTCTTGCATAGAAGAGTCAACCTAGGAAAAAGGAGAGCCTT
CTTAAATGCTTAGCAGATCTCTTCCATAGCATAGCCACTCAGAAGAAAAAGTTGGAGTAATACCTCCTAAGAAGTTCATC
ACAAGATTACGGAAAGAAAATGAGCTTTTGACAACTACATGCAACAAGATCCCCATGAATTCTTAAATTACTTAGTAATA
CAATTGCTGATATTTTACAAGAAGAGAGAAAGCAGGAAGAACAAAATGGCCGCTTACCTAATGGTAATATTAATAATGAG
AATAATAACAGCACCCCAGACCCAAAGCGGGTTCATGAGATTTTTCAGGGAACATTAACTAATGAAACCAGATGTCTTAC
TTGTGAAACTATAAGCAGCAAAGATGAAGATTTTTTAGACCTTTCTGTTGACGTGGAACAAAATACATCAATTACTCACT
GCTTAAAGGCTTTCAGCAACACAGAAACTCTATGCAGTGAACACGAGTATTACTGTGAAGAGTGTCGCAGCAAACAGGAA
GCACACAAATGGATGAAAGTTTAAAAACTGCCCATGATTCTAGCTCTACACCTGAAGAGATTTAAATATATGGATCAACT
TTATTGATTTACAAAACTCTCTTACCAAGTAGTTTTTCCTTTAAAACTTAGTCTATTTAACACTTCAGGTGATGCCACCA
ATCCAGACAGAATGTACAGCCTTGTTGCTGTTGTGGTTCACTGCGGA

Alignment

ORF - retro_pabe_2705 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.37 %
• Parental protein coverage: 83.78 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEILMTVSKFASICTMGANASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAY
          M.ILMTVSKFASICTMGANASALEKEIGPEQFPVNEHYFGLV.FGNTCYCNSVLQALYFCRPFRE.VLA.
Retrocopy M*ILMTVSKFASICTMGANASALEKEIGPEQFPVNEHYFGLVSFGNTCYCNSVLQALYFCRPFRETVLA*

Parental  KSQPRKKESLLTCLADLFHSIATQKKK-VGVIPPKKFITRLRKENEL-FDNYMQQDAHEFLNYLL-NTIA
          KSQPRKKESLL.CLADLFHSIATQKKK.VGVIPPKKFITRLRKENEL.FDNYMQQD.HEFLNYL..NTIA
Retrocopy KSQPRKKESLLKCLADLFHSIATQKKK<VGVIPPKKFITRLRKENEL<FDNYMQQDPHEFLNYLV<NTIA

Parental  DILQEERKQEKQNGRLPNGNIDNENNNSTPDPTWVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVDVE
          DILQEERKQE.QNGRLPNGNI.NENNNSTPDP..VHEIFQGTLTNETRCLTCETISSKDEDFLDLSVDVE
Retrocopy DILQEERKQEEQNGRLPNGNINNENNNSTPDPKRVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVDVE

Parental  QNTSITHCLRGFSNTETLCSEYKYYCEECRSKQEAHKRMKVKKLPMILALHLKRFKYMDQLHRYTKLSYR
          QNTSITHCL..FSNTETLCSE..YYCEECRSKQEAHK.MKV.KLPMILALHLKRFKYMDQL...TKLSY.
Retrocopy QNTSITHCLKAFSNTETLCSEHEYYCEECRSKQEAHKWMKV*KLPMILALHLKRFKYMDQLY*FTKLSYQ

Parental  VVFPLELRLFNTSGDATNPDRMYDLVAVVVHCG
          VVFPL.L.LFNTSGDATNPDRMY.LVAVVVHCG
Retrocopy VVFPLKLSLFNTSGDATNPDRMYSLVAVVVHCG

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	0.44 RPM	26.59 RPM
SRP007412_cerebellum	0.85 RPM	22.62 RPM
SRP007412_heart	0.18 RPM	13.46 RPM
SRP007412_kidney	0.17 RPM	17.57 RPM
SRP007412_liver	0.24 RPM	12.36 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2705 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2705 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2705 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3266
Pan troglodytes	retro_ptro_2209
Gorilla gorilla	retro_ggor_2223

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019344	5 retrocopies	retro_cjac_2734, retro_cjac_3901, retro_cjac_3964, retro_cjac_3965, retro_cjac_4011,
Homo sapiens	ENSG00000152484	4 retrocopies	retro_hsap_2328, retro_hsap_3266, retro_hsap_4726, retro_hsap_4918,
Microcebus murinus	ENSMICG00000006269	2 retrocopies	retro_mmur_1167, retro_mmur_1187,
Macaca mulatta	ENSMMUG00000021425	1 retrocopy	retro_mmul_937,
Nomascus leucogenys	ENSNLEG00000000323	3 retrocopies	retro_nleu_1817, retro_nleu_1995, retro_nleu_2426,
Otolemur garnettii	ENSOGAG00000030639	1 retrocopy	retro_ogar_2897,
Pongo abelii	ENSPPYG00000005232	3 retrocopies	retro_pabe_2110, retro_pabe_2705 , retro_pabe_3672,
Pan troglodytes	ENSPTRG00000005727	3 retrocopies	retro_ptro_1701, retro_ptro_2209, retro_ptro_3143,
Tupaia belangeri	ENSTBEG00000012960	2 retrocopies	retro_tbel_3285, retro_tbel_4692,