RetrogeneDB ID: retro_pabe_304

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:141869381..141870328(+)
• Located in intron of: ENSPPYG00000001183

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBA2
• Ensembl ID: ENSPPYG00000009837
• Aliases: None
• Description: ubiquitin-like modifier activating enzyme 2 [Source:HGNC Symbol;Acc:30661]

Sequence

>retro_pabe_304
AGCACTGAGACTCTGAGAGTTCATTTAGCAGAAAAGGGGGATGGAGCTGAGCTCATATGGGATAAGGATGACCCACATGC
AATGGATTTTGTCACCTCTGCTACAAACCTCAGGATGCATATTTTCAGTATGAATATGAAGAGTAGATTTGATATCAAAT
CAATGGCAGGGGATATTATTCCTGCTATTGCTACTACTAATGCAGTGATTGCTGGGTTGACGGTATTGGAAAGATTGAAG
ATCTTATTAGGAAAAATAGACCAGTGCAGAACAATTGTTTTGAATAAACAACCAAATCCAAGAAAGCAGTTTCTTGTGCC
TTGTGCACTGGATCCTCCCAACCCCAATTGTTATGTATGTGCCAGCAAACCAGAGGTGATTGTATGGCTGAATGTCCATA
AAGTGACTGTTCTCACTTTACAAGACAAGGTAGTGAAAGAAAAATTTGCTGTGGTAGCACCAGATGTCCAAATTGAAGAT
GGGAAAGGAACAATCCTAATATCTTCCGAAGAGAGAGAGACAGAAGCTAATAATCACAAGAAGTTGTCAGAATTTGGAAT
GAGAAATTGCAGCTGGCTTCAAGCAGATTACTTCCTCCAGGACTATACTTTATTGATCAACATCCTTCATAGTGAAGACC
TAGGAAAGGATGTTGAATTTGAAGTGTTGGTGATGCCCCAGAAACAGTGGGGCCAAAACAAGCTGAAGATGCTGCCAAAA
GCATAACCAATGACAGTAATGATGGAGCTCAGCCTTCCACCTCCACAGCTCAAGAGCAAGATTATGTTCTCACAGTTGAT
TCGGATGAAGAAGATTCTTCAAAGAATGCTGACGTCAGTGAAGAAGAGAGAAGCCACAAGAGGAAATCAGACGAGAAAGA
GAATCTCAGAGCAAAGAGGTCACGTATAGAACAGAAGGAAGAGCTTGATGATGTCATAGCATTAGAT

Alignment

ORF - retro_pabe_304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.54 %
• Parental protein coverage: 58.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SIETLRVHLAEKGDGAELIWDKDDPSAMDFVTSAANLRMHIFSMNMKSRFDIKSMAGNIIPAIATTNAVI
          S.ETLRVHLAEKGDGAELIWDKDDP.AMDFVTSA.NLRMHIFSMNMKSRFDIKSMAG.IIPAIATTNAVI
Retrocopy STETLRVHLAEKGDGAELIWDKDDPHAMDFVTSATNLRMHIFSMNMKSRFDIKSMAGDIIPAIATTNAVI

Parental  AGLIVLEGLKILSGKIDQCRTIFLNKQPNPRKKLLVPCALDPPNPNCYVCASKPEVTVRLNVHKVTVLTL
          AGL.VLE.LKIL.GKIDQCRTI.LNKQPNPRK..LVPCALDPPNPNCYVCASKPEV.V.LNVHKVTVLTL
Retrocopy AGLTVLERLKILLGKIDQCRTIVLNKQPNPRKQFLVPCALDPPNPNCYVCASKPEVIVWLNVHKVTVLTL

Parental  QDKIVKEKFAMVAPDVQIEDGKGTILISSEEGETEANNHKKLSEFGIRNGSRLQADDFLQDYTLLINILH
          QDK.VKEKFA.VAPDVQIEDGKGTILISSEE.ETEANNHKKLSEFG.RN.S.LQAD.FLQDYTLLINILH
Retrocopy QDKVVKEKFAVVAPDVQIEDGKGTILISSEERETEANNHKKLSEFGMRNCSWLQADYFLQDYTLLINILH

Parental  SEDLGKDVEFEV-VGDALEKVGPKQAEDAAKSITNGSDDGAQPSTSTAQEQDDVLIVDSDEEDSSNNADV
          SEDLGKDVEFEV.VGDA.E.VGPKQAEDAAKSITN.S.DGAQPSTSTAQEQD.VL.VDSDEEDSS.NADV
Retrocopy SEDLGKDVEFEV<VGDAPETVGPKQAEDAAKSITNDSNDGAQPSTSTAQEQDYVLTVDSDEEDSSKNADV

Parental  SEEERSRKRKLDEKENLSAKRSRIEQKEELDDVIALD
          SEEERS.KRK.DEKENL.AKRSRIEQKEELDDVIALD
Retrocopy SEEERSHKRKSDEKENLRAKRSRIEQKEELDDVIALD

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	0.00 RPM	37.76 RPM
SRP007412_cerebellum	0.00 RPM	54.60 RPM
SRP007412_heart	0.00 RPM	20.44 RPM
SRP007412_kidney	0.00 RPM	23.14 RPM
SRP007412_liver	0.00 RPM	21.54 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_304 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_304 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_304 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
Choloepus hoffmanni	ENSCHOG00000011975	3 retrocopies	retro_chof_1034, retro_chof_548, retro_chof_848,
Myotis lucifugus	ENSMLUG00000003047	1 retrocopy	retro_mluc_286,
Monodelphis domestica	ENSMODG00000011934	1 retrocopy	retro_mdom_1509,
Pongo abelii	ENSPPYG00000009837	1 retrocopy	retro_pabe_304 ,
Rattus norvegicus	ENSRNOG00000021113	1 retrocopy	retro_rnor_939,
Sus scrofa	ENSSSCG00000002876	1 retrocopy	retro_sscr_941,