RetrogeneDB ID: retro_pabe_2224

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:75539314..75540253(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNPC3
• Ensembl ID: ENSPPYG00000001102
• Aliases: None
• Description: RNA-binding protein 40 [Source:RefSeq peptide;Acc:NP_001126576]

Sequence

>retro_pabe_2224
TCTAATGACCCTGTTGAAGACGATAAAGAAAAGAAATAACTTGGTTATTTAACAGTAGAAAATGGAATTGCACCAAACCA
TGGGCTGACTTTTCCTAATTCATGCCTCAAGTATATGTACCCACCACCTTCCAGAACAATCCTAGCAAACAGAGTAAATG
CTTTGGCAAGCATGCCTAAGTTCTATGTACAGGTCCTTCATCTTATGAATAAAATGAATTTGCCCACAGCTTTTAGATCA
ATTACTGTGCGACCTCCCATCTATGGAGACCATATGCCATTGCATGCACCTCTTCCACCCACATCTCCTCAGCCACCTGA
GGAACCTCCTTGACCAGACGACGATGAGGAATTATCTAGTGAAGAATTAGAAGATGACAGCAGTGATGATGAGGACCAAC
AGAGAATGAACAAACTAATGGAACTAGCAAATCTTCAGCCCCAAAGACCCAAAACAGTAAAGCAGCGCCATGTGAGAAAA
AAAGAGAAAAATAAAGGATATGTTGAACATACTTTCATGTCCTTCACAAAACAGTTTACATCTAGTGTTGTTACCTTCGG
ATGTATTTGACCAACCACAACCTGTAGGTAATAAAATAATTGAATGCCATATATCTACCGACATGCCAGCTGCATTTAAG
AAAGATTTAGAGAAGAAACAAAATTGTGAGAAACAAATAACGATTTACCTGTTACTGAAGCTGATGCATCCAATACAGGA
TTTGGAAAAATCTTTCCGAAACCTAATTTGAACATCACAGAAGAGATTTAAAAAGACTCTGATGAAATGCCATCAGAATG
TATTTCTCGAAGGGAATTGGAAAAGGACAGAATTTCTAGAGAAGAAATGGAAACACTTTCAGTTTTCAGAAGTTATGAAC
CTGGTGAACCAAACTGTAGAATTTATGTAAAGAATTTAGCTAAACATGTTCAAGAAAAG

Alignment

ORF - retro_pabe_2224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.91 %
• Parental protein coverage: 71.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SDDPVEDDKEKKELGYLTVENGIAPNHGLTFPLNSCLKYMYPPP-FQHNPSQHRKC-LASVPKFYVQVLH
          S.DPVEDDKEKK.LGYLTVENGIAPNHGLTFP.NSCLKYMYPPP.FQ.NPS...KC.LAS.PKFYVQVLH
Retrocopy SNDPVEDDKEKK*LGYLTVENGIAPNHGLTFP-NSCLKYMYPPP<FQNNPSKQSKC>LASMPKFYVQVLH

Parental  LMNKMNLPTPFGPITARPPMYEDYMPLHAPLPPTSPQPPEEPPLPEEDEELSSEESEYESTDDEDRQRMN
          LMNKMNLPT.F..IT.RPP.Y.D.MPLHAPLPPTSPQPPEEPP.P..DEELSSEE.E..S.DDED.QRMN
Retrocopy LMNKMNLPTAFRSITVRPPIYGDHMPLHAPLPPTSPQPPEEPP*PDDDEELSSEELEDDSSDDEDQQRMN

Parental  KLMELANLQPKRPKTIKQRHVR-KKRKIKDMLNTPLCPSHSSLHPVLLPSDVFDQPQPVGNKRIEFHIST
          KLMELANLQP.RPKT.KQRHVR.KKRKIKDMLN...CPS..SLH.VLLPSDVFDQPQPVGNK.IE.HIST
Retrocopy KLMELANLQPQRPKTVKQRHVR>KKRKIKDMLNILSCPSQNSLHLVLLPSDVFDQPQPVGNKIIECHIST

Parental  DMPAAFKKDLEKEQNCE-EKNHDLPATEVDASNIGFGKIFPKPNLDITEEIKEDSDEMPSECISRRELEK
          DMPAAFKKDLEK.QNCE.E.N.DLP.TE.DASN.GFGKIFPKPNL.ITEEI..DSDEMPSECISRRELEK
Retrocopy DMPAAFKKDLEKKQNCE<ETNNDLPVTEADASNTGFGKIFPKPNLNITEEI*KDSDEMPSECISRRELEK

Parental  GRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVEEK
          .RISREEMETLSVFRSYEPGEPNCRIYVKNLAKHV.EK
Retrocopy DRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEK

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	12.33 RPM
SRP007412_cerebellum	0.12 RPM	19.21 RPM
SRP007412_heart	0.00 RPM	4.27 RPM
SRP007412_kidney	0.17 RPM	14.35 RPM
SRP007412_liver	0.06 RPM	7.37 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2224 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2224 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2224 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2800
Pan troglodytes	retro_ptro_1897
Macaca mulatta	retro_mmul_1435
Callithrix jacchus	retro_cjac_1397

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000035686	1 retrocopy	retro_cjac_1397,
Homo sapiens	ENSG00000185946	1 retrocopy	retro_hsap_2800,
Macaca mulatta	ENSMMUG00000018039	1 retrocopy	retro_mmul_1435,
Nomascus leucogenys	ENSNLEG00000012013	1 retrocopy	retro_nleu_1539,
Nomascus leucogenys	ENSNLEG00000015566	1 retrocopy	retro_nleu_1538,
Pongo abelii	ENSPPYG00000001102	1 retrocopy	retro_pabe_2224 ,
Pan troglodytes	ENSPTRG00000033902	1 retrocopy	retro_ptro_1897,