RetrogeneDB ID: retro_pabe_2957

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:57029099..57029901(-)
• Located in intron of: None

Retrocopy information

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

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_2957
GGCAACAGCACTGCCAGCGCCGGGCCCAGGAAGCTCGGCGGCCCGGCGGCTGCAGCTGCGGCTGCAGTGGTGACTAGGAC
AGCGTGGAGCTCGACTGGGACCCCTGCGGGGACAAGCGCGCGGGGCACCAAGGAGCGCGTCAAACTTAAAGGGTCAAAGT
GCAACGGGCAGCTTTTGATTTTGGGGGCAACCAACTGGGACATGACTGGTCGAAAGGAAGTGCCTAAACAGCAAGCTGCT
TACCGCAATCTCGGTCAGAATTTGTGGGGTCCCCACAGGTATGGCTGTCTAGCGGGGGTCCGGATACGGACAGTGGTCTC
AGGTTCCTGTGCTGCACACAGCCTCCTCATCACTATGGAAGGGAAGCTGTGGAGTTGGGGTCGAAATGAGAAGGGGCAGC
TGGGACATGGCGACACCAAGAGAGTAGAGGCCCCCAGACTCATCGAGGGTCTCTGCCATGAAGTGATCATGTCTGCAACA
TGTGGGTGGAACCACACCTTGGCCTTGACGGAAACGGGCTCTGTGTTTGCGTTTGGGGAGAACAAGATGGGGCAGCTGGG
CCTTGCCAACCAGACAGACGCTGTGCAGCCCCGCGCAGATAATGTATAACGGCCAGCCAATTACCAAAATGGCCTGTGGG
GCTGAATTCAGTATAATGGACTGAAAAGGAAACCTCTGTTCCTTTGGGTGCCCTGAATATGGTCAGCTGGGACACAACTC
GGATGGGAAGTTCATCTTCGGGGCACAGCGGATAGAGTATGACTGCGAACTGGTACCCCCGCGATTGGCCATATTCATTG
AG

Alignment

ORF - retro_pabe_2957 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.48 %
• Parental protein coverage: 51.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSSGDEDGLELDGAPGGGKRAARPATAGKAGGXXXXXXXXXGRSDVRRXXXXKCKGQLLIFGATNWDLIG
          G.S....G....G.P.....AA...................G..........KC.GQLLI.GATNWD..G
Retrocopy GNSTASAGPRKLGGPAAAAAAAVVTRTAWSSTGTPAGTSARGTKERVKLKGSKCNGQLLILGATNWDMTG

Parental  RKEVPKQQAAYRNLGQNLWGPHRYGCLAGVRVRTVVSGSCAAHSLLITTEGKLWSWGRNEKGQLGHGDTK
          RKEVPKQQAAYRNLGQNLWGPHRYGCLAGVR.RTVVSGSCAAHSLLIT.EGKLWSWGRNEKGQLGHGDTK
Retrocopy RKEVPKQQAAYRNLGQNLWGPHRYGCLAGVRIRTVVSGSCAAHSLLITMEGKLWSWGRNEKGQLGHGDTK

Parental  RVEAPRLIEGLSHEVIVSAACGRNHTLALTETGSVFAF-GENKMGQLGLGNQTDAVPSPAQIMYNGQPIT
          RVEAPRLIEGL.HEVI.SA.CG.NHTLALTETGSVFAF.G....G...L........SPAQIMYNGQPIT
Retrocopy RVEAPRLIEGLCHEVIMSATCGWNHTLALTETGSVFAF>GRTRWGSWALPTR-QTLCSPAQIMYNGQPIT

Parental  KMACGAEFSMIMDCKGNLYSFGCPEYGQLGHNSDGKFIARAQRIEYDCELVPRRVAIFIE
          KMACGAEFS.IMD.KGNL.SFGCPEYGQLGHNSDGKFI..AQRIEYDCELVP.R.AIFIE
Retrocopy KMACGAEFS-IMD*KGNLCSFGCPEYGQLGHNSDGKFIFGAQRIEYDCELVPPRLAIFIE

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	0.22 RPM	44.01 RPM
SRP007412_cerebellum	0.12 RPM	27.97 RPM
SRP007412_heart	0.09 RPM	8.79 RPM
SRP007412_kidney	0.07 RPM	40.17 RPM
SRP007412_liver	0.03 RPM	14.99 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2957 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2957 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2957 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3597
Pan troglodytes	retro_ptro_2434

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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,