RetrogeneDB ID: retro_pabe_3672

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:88654694..88655801(+)
• Located in intron of: None

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_3672
ATGGAAATCCTAATGACAGTCTCCAAATTCGCCTCCATCTGTACCATGGGCGCCAATGCTTCGGCATTAGAGAAAGAGAT
GGGTCCAGAACAGTTTCCGGTCAATGAGCATTATTTTGGATTAGTCAGTTTTGGGAATACCTGCTACTGCAATTCAGTTC
TTCAAGCACTTCATTTTTGTCGTCCATTTCGGGAAAAAGTTCTTGCATATAAGAGTCAACCTAGGAAAAAGGAGAGCCTT
CTTACATGCTTAGCAGATCTCTTCCACAGCATAGCCACTCAGAAGAAAAAGGTTGGAGTAATACCTCCTAAGAAGTTCAT
CGCAAGATTACGGAAAGAAAATGAGCTTTTCGACAACTACATGCAACAAGATGCCCATGAATTCTTAAATTACCTACTAA
ATACAATTGGTGATATTTTACAAGAAGAGAGAAAGCAGGAAAAACAAAATGGTCCCTAACCTAATGATAATATTGACAAT
GAAAATAATAGCAGCACACCAGACCCAACGTGGGTTCATGAGATTTTTCAGGGAACATTAACTAATGAAACCAGACGTCT
TACTTGTGAAACTATAAGCAGCAAAGATGAAGATTTTTTAGACCTTTCTGTTGACGTGGAACAAAATACATCAATTACTC
ACTGCTTAAGGGGTTTCAGCAACACAGAAACTATGCAGTGAATACAAGTATTACTATGGAGAGTGTCGCAGCAAACAGGA
AGCACACAAACGGATGAAAGTTTAAAAACTGCCCATGATTCTAGCTCTACACTTGAAGAGATTTAAATATATGGATCAAC
TTCATCGACATACAAAACTTTCTTACCGGGTAGTTTTTCCTTTAGAACTTCGTCTATTTAACACTTCAGGTGATGCCACC
AATCCAGACAGAATGTATGACCTTGTTGCTGTTGTGGTTCACTGTGGAAGTGGTTCCAATCGAGGCCATTATATTGCAAC
AGTTAAGAGTCATGATTTTTGGTTGTTGTTTGATGACGATATTGTAGAAAAAATAGATGCACAAGCTGTTGAAGAATTCT
ACGGGTTGACATCAGATACTCAAAGAAATCTGAGTCTGGTTACATCCTTTTCTATCAGTCTCGGGAC

Alignment

ORF - retro_pabe_3672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.3 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEILMTVSKFASICTMGANASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAY
          MEILMTVSKFASICTMGANASALEKE.GPEQFPVNEHYFGLV.FGNTCYCNSVLQAL.FCRPFREKVLAY
Retrocopy MEILMTVSKFASICTMGANASALEKEMGPEQFPVNEHYFGLVSFGNTCYCNSVLQALHFCRPFREKVLAY

Parental  KSQPRKKESLLTCLADLFHSIATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADIL
          KSQPRKKESLLTCLADLFHSIATQKKKVGVIPPKKFI.RLRKENELFDNYMQQDAHEFLNYLLNTI.DIL
Retrocopy KSQPRKKESLLTCLADLFHSIATQKKKVGVIPPKKFIARLRKENELFDNYMQQDAHEFLNYLLNTIGDIL

Parental  QEERKQEKQNGRLPNGNIDNENNNSTPDPTWVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVDVEQNT
          QEERKQEKQNG..PN.NIDNENN.STPDPTWVHEIFQGTLTNETR.LTCETISSKDEDFLDLSVDVEQNT
Retrocopy QEERKQEKQNGP*PNDNIDNENNSSTPDPTWVHEIFQGTLTNETRRLTCETISSKDEDFLDLSVDVEQNT

Parental  SITHCLR-GF-SNTETLCSEYKYYCEECRSKQEAHKRMKVKKLPMILALHLKRFKYMDQLHRYTKLSYRV
          SITHCLR.GF.S.T..LCSEYKYY..ECRSKQEAHKRMKV.KLPMILALHLKRFKYMDQLHR.TKLSYRV
Retrocopy SITHCLR<GF<SATQKLCSEYKYYYGECRSKQEAHKRMKV*KLPMILALHLKRFKYMDQLHRHTKLSYRV

Parental  VFPLELRLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAIVKSHDFWLLFDDDIVEKIDAQAIEEFY
          VFPLELRLFNTSGDATNPDRMYDLVAVVVHCGSG.NRGHYIA.VKSHDFWLLFDDDIVEKIDAQA.EEFY
Retrocopy VFPLELRLFNTSGDATNPDRMYDLVAVVVHCGSGSNRGHYIATVKSHDFWLLFDDDIVEKIDAQAVEEFY

Parental  GLTSD-ISKNSESGYILFYQSRD
          GLTSD..SK.SESGYILFYQSRD
Retrocopy GLTSD<YSKKSESGYILFYQSRD

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	0.83 RPM	26.59 RPM
SRP007412_cerebellum	0.85 RPM	22.62 RPM
SRP007412_heart	0.42 RPM	13.46 RPM
SRP007412_kidney	0.73 RPM	17.57 RPM
SRP007412_liver	0.31 RPM	12.36 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3672 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3672 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3672 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4726
Homo sapiens	retro_hsap_4918
Pan troglodytes	retro_ptro_3143
Gorilla gorilla	retro_ggor_2937

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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,