RetrogeneDB ID: retro_pabe_3766

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:63177141..63178007(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000013118
• Aliases: None
• Description: None

Sequence

>retro_pabe_3766
ATGCCCAAAGATTTAGCTTTGGAGTCAAACCCTTCTGACCATCCAGGGGCAAGCACAATTTTACTGCGCAAATCTCAAAC
GGATGTGAGAGAAAAGAGGAAGAGCAACCATTTAAACCATGTATCTCCAGGGCAGCTTACTAAAAAGTATAGCTCATGCT
CAACAATATTTCTATACGACGGCACAGTCAACCAGCCTAATCTTAGAACCACAGTAAAATGTGTGACCTTAGCAATATAT
CACCACATAAAGAACAGAGATGCAAATAGATCCCTGGATATTTTTGATGAGAGATCACATCCACTTACATGAGAAAAAGT
TCCAGAAGAACAGTTTAAGCATGATCCTGAGCACAAATTTATTTACAGATTTGTTCATACTCCTTTTAGTGCCGCACAGC
TAACAGCTGAATGTGCAATAGTAACTTTGGTTTACTTAGAAAAGCTTTTAACTTATGCTGAAACCAACATTTGTCCCACT
AACTGGAAAAGGATTGGTCTGGGAGCCATTCTTCTTGCCTCCAAGGTTTGGGACCATCAAGCTGTATGGAATATGGACTA
CTGCCAGATCTTCAAGGACATTACAGGTGAGGACATGAATGAAATGGAAAGGCATTTTTTGAAGCTTCTTCAGTTTAATA
TTAATGTTCCTGCCAGTGTTTATGCCAAATACTACTTTGATCTTCGCTCCTTAGCAGATGACAATAACCTGAATTTTCTA
TTTGCTCCTTTTAGCAAAAAAAGAGCACAGAAACTAGAGGCTATTTCTAGATTGTGTGAAGACAAAGACTTGTGTAGAGC
CCTATGAGAAGGTCTTTCAGCACTGATGACTTCATTGGTATTCAGCACTCTAAAGCCATCCTCTCT

Alignment

ORF - retro_pabe_3766 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPEDLALESNPSDHPRASTIFLSKSQTDVREKRKSNHLNHVSPGQLTKKYSSCSTIFLDDSTVSQPNLRT
          MP.DLALESNPSDHP.ASTI.L.KSQTDVREKRKSNHLNHVSPGQLTKKYSSCSTIFL.D.TV.QPNLRT
Retrocopy MPKDLALESNPSDHPGASTILLRKSQTDVREKRKSNHLNHVSPGQLTKKYSSCSTIFLYDGTVNQPNLRT

Parental  TVKCVTLAIYYHIKNRDANRSLDIFDERSHPLTREKVPEEYFKHDPEHKFIYRFVRTLFSAAQLTAECAI
          TVKCVTLAIY.HIKNRDANRSLDIFDERSHPLT.EKVPEE.FKHDPEHKFIYRFV.T.FSAAQLTAECAI
Retrocopy TVKCVTLAIYHHIKNRDANRSLDIFDERSHPLT*EKVPEEQFKHDPEHKFIYRFVHTPFSAAQLTAECAI

Parental  VTLVYLERLLTYAEIDICPTNWKRIVLGAILLASKVWDDQAVWNVDYCQILKDITVEDMNEMERHFLELL
          VTLVYLE.LLTYAE..ICPTNWKRI.LGAILLASKVWD.QAVWN.DYCQI.KDIT.EDMNEMERHFL.LL
Retrocopy VTLVYLEKLLTYAETNICPTNWKRIGLGAILLASKVWDHQAVWNMDYCQIFKDITGEDMNEMERHFLKLL

Parental  QFNINVPASVYAKYYFDLRSLADDNNLNFLFAPLSKERAQNLEAISRLCEDKDLCRA-AMRRSFSADNFI
          QFNINVPASVYAKYYFDLRSLADDNNLNFLFAP.SK.RAQ.LEAISRLCEDKDLCRA..MRRSFS.D.FI
Retrocopy QFNINVPASVYAKYYFDLRSLADDNNLNFLFAPFSKKRAQKLEAISRLCEDKDLCRA<PMRRSFSTDDFI

Parental  GIQRSKAILS
          GIQ.SKAILS
Retrocopy GIQHSKAILS

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	2.49 RPM
SRP007412_cerebellum	0.00 RPM	1.22 RPM
SRP007412_heart	0.03 RPM	1.69 RPM
SRP007412_kidney	0.00 RPM	2.52 RPM
SRP007412_liver	0.00 RPM	3.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3766 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3766 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3766 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002901	1 retrocopy	retro_cjac_569,
Homo sapiens	ENSG00000163249	3 retrocopies	retro_hsap_1629, retro_hsap_1984, retro_hsap_4845,
Macaca mulatta	ENSMMUG00000020211	1 retrocopy	retro_mmul_2587,
Mus musculus	ENSMUSG00000070871	1 retrocopy	retro_mmus_3072,
Nomascus leucogenys	ENSNLEG00000007131	3 retrocopies	retro_nleu_1164, retro_nleu_2902, retro_nleu_430,
Pongo abelii	ENSPPYG00000013118	3 retrocopies	retro_pabe_1345, retro_pabe_3766 , retro_pabe_76,