RetrogeneDB ID: retro_pabe_748

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:13809569..13810770(-)
• Located in intron of: ENSPPYG00000003166

Retrocopy information

• Ensembl ID: ENSPPYG00000003167
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RCC2
• Ensembl ID: ENSPPYG00000025834
• Aliases: None
• Description: regulator of chromosome condensation 2 [Source:HGNC Symbol;Acc:30297]

Sequence

>retro_pabe_748
GTGCCTAAACAGGAAGATGCTTACAGTAATATCGGTCAGAATTTGTGGGGGCCCCATAGGTATGGGTGCCTGGCAGGGGT
CCAGGTGCAGACAGTGGTCTCCGGCTCCTGTGCTGCACACAGCCTCCTCATCACCACAGAAGGGAAGCTGTGGAGCTGGG
GTCGAAATGAGAAGGCGCAGCTGGGACATGGTGACATCAAGAGTAGAAGCCCCCAGACTCATCGAGGGTCTCAGCCACGA
AGTGATTGTGTCTGCAGCATGTGGGCAGAACCACACCTTGGCCTTGACGGAAACAGGCTCCGTGTTTGCATTTGGGGAAA
ACAAGATGGGGCAGCTGGGCCTTGGCAACCAGACGGACGCTGTCCCTAGCCCTGTGCAGATTAATGTACAACAGCCAGCC
AATTACCAAAATGGCCTGTGGGGCTGAATTCAGTATGATAATGGACTGCAAAGGAAACCTCTATTCCTTTGGGGGCCCTG
AATATGGTCAGCTGGGACACAACTCAATGGGAAGTTAATTGCCTGGGCACAGCGGATAGAGTGTGACTGCGAACTAGTTC
CCCAGCAAGTGGCCATCTTCATTAAGAAGACGAAAGACGGACAGATTCTGCCTCTACCAAACTTGGTTATGTGAGACGTG
TCCTGTGGTGCTAACCACACGCTAGTTCTGGACTCCCAGAAGTGAGTCTTCTCCTGGGGCTTCGGTGGCTATGGCTGGCT
GGGCTACACAGAGCAGAAGGATGAGATGGTCCCCCGCCTGGTGAAGCTGTTTGGCTTCCCTGGGCATGGGGCTTCCCAGA
TCTATGCTGGTTGCGCCTGCTCCTTTGCCATCAGTGAAGTGGGTGGTCTGTTTTTCTGGGGGGCTACCAACACCTCCCGT
GAATCTTCCATGTACCCAAAAGCAGTGCAGGACCTCTGCGGCTGGAGAATCCGGAGCCTGGCTTGTGGGAAGAGCAGCAT
CATTGTGGCTGCCAAGGAGAGCACCGTCAGGTGGGGCCCGTCACCGACCTTTGGGGAACTGGGCTACAGGGACCACAAGC
CCCAGTCTTCCACTGCAGCCCAGGAGGTGAAGATGCTGCATGGCATTTTCTCAGAGCAGGTTGCCGTGGGCTACTCACAC
TCCTTGGTGATAACAAGAGATGAAAGTGAGACTGAGAAAGAAAAGATCAAGAAACTGCCAGAATACAACCCCCAAACCCT
C

Alignment

ORF - retro_pabe_748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.13 %
• Parental protein coverage: 76.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VPKQQAAYRNLGQNLWGPHRYGCLAGVRVRTVVSGSCAAHSLLITTEGKLWSWGRNEKGQLGHGDTKRVE
          VPKQ..AY.N.GQNLWGPHRYGCLAGV.V.TVVSGSCAAHSLLITTEGKLWSWGRNEK.QLGHGD.K...
Retrocopy VPKQEDAYSNIGQNLWGPHRYGCLAGVQVQTVVSGSCAAHSLLITTEGKLWSWGRNEKAQLGHGDIKS-R

Parental  APR-LIEGLSHEVIVSAACGRNHTLALTETGSVFAFGENKMGQLGLGNQTDAVPSPAQI-MYNGQPITKM
          .P..LIEGLSHEVIVSAACG.NHTLALTETGSVFAFGENKMGQLGLGNQTDAVPSP.QI.MYN.QPITKM
Retrocopy SPQ>LIEGLSHEVIVSAACGQNHTLALTETGSVFAFGENKMGQLGLGNQTDAVPSPVQI>MYNSQPITKM

Parental  ACGAEFSMIMDCKGNLYSFGCPEYGQLGHNS-DGKFIARAQRIEYDCELVPRRVAIFIEKTKDGQILPVP
          ACGAEFSMIMDCKGNLYSFG.PEYGQLGHNS..GK.IA.AQRIE.DCELVP..VAIFI.KTKDGQILP.P
Retrocopy ACGAEFSMIMDCKGNLYSFGGPEYGQLGHNS<NGKLIAWAQRIECDCELVPQQVAIFIKKTKDGQILPLP

Parental  NVVVRDVACGANHTLVLDSQKRVFSWGFGGYGRLGHAEQKDEMVPRLVKLFDFPGRGASQIYAGYTCSFA
          N.V..DV.CGANHTLVLDSQK.VFSWGFGGYG.LG..EQKDEMVPRLVKLF.FPG.GASQIYAG..CSFA
Retrocopy NLVM*DVSCGANHTLVLDSQK*VFSWGFGGYGWLGYTEQKDEMVPRLVKLFGFPGHGASQIYAGCACSFA

Parental  VSEVGGLFFWGATNTSRESTMYPKAVQDLCGWRIRSLACGKSSIIVAADESTISWGPSPTFGELGYGDHK
          .SEVGGLFFWGATNTSRES.MYPKAVQDLCGWRIRSLACGKSSIIVAA.EST..WGPSPTFGELGY.DHK
Retrocopy ISEVGGLFFWGATNTSRESSMYPKAVQDLCGWRIRSLACGKSSIIVAAKESTVRWGPSPTFGELGYRDHK

Parental  PKSSTAAQEVKTLDGIFSEQVAMGYSHSLVIARDESETEKEKIKKLPEYNPRTL
          P.SSTAAQEVK.L.GIFSEQVA.GYSHSLVI.RDESETEKEKIKKLPEYNP.TL
Retrocopy PQSSTAAQEVKMLHGIFSEQVAVGYSHSLVITRDESETEKEKIKKLPEYNPQTL

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	0.33 RPM	44.01 RPM
SRP007412_cerebellum	0.49 RPM	27.97 RPM
SRP007412_heart	0.03 RPM	8.79 RPM
SRP007412_kidney	0.73 RPM	40.17 RPM
SRP007412_liver	0.15 RPM	14.99 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_748 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_748 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_748 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001396	1 retrocopy	retro_dnov_2692,
Homo sapiens	ENSG00000179051	3 retrocopies	retro_hsap_2677, retro_hsap_3073, retro_hsap_3597,
Gorilla gorilla	ENSGGOG00000015263	1 retrocopy	retro_ggor_2112,
Nomascus leucogenys	ENSNLEG00000007783	2 retrocopies	retro_nleu_2483, retro_nleu_298,
Otolemur garnettii	ENSOGAG00000014544	1 retrocopy	retro_ogar_2967,
Pongo abelii	ENSPPYG00000025834	3 retrocopies	retro_pabe_2547, retro_pabe_2957, retro_pabe_748 ,
Pan troglodytes	ENSPTRG00000000247	3 retrocopies	retro_ptro_1804, retro_ptro_2072, retro_ptro_2434,
Rattus norvegicus	ENSRNOG00000006327	1 retrocopy	retro_rnor_1378,