RetrogeneDB ID: retro_pabe_76

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19_random:637673..638528(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000010520
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_pabe_76
GATTTAACTTTGGAGTCAAACCCTTCTGACCATCCAAGGGCAAGCACAATTTTCCTGAGCAAATCTCAAACCAATGTGCG
AGAAAAGAGGAAGAGCAACCACTTAAATCATCTATCTCTAGGGCAGCTTACTAAAAAGTATAGCTTATGCTCAACAATAT
TTCTAGATGACAGAACAGTCAGCCAGCCTAACCTTAGAACCACTGTAAAATGTGTGACCTTAGAAATATATTACCACATA
AAGAACAGAGATGCAAATAGATCCCTGGATATTTTTGATGAGAGATCACATCCCCTTACACGAGAAAAAGTTCCACAGGA
ATACTTTAAGCATGATCCTGAGCACAAATTTATTTACAGATTTGTTCGTACTCTTTTTAGTGCTGCACAGCTAACAGCTG
AATGTCCAATAGTAACTCTGGTTTACTTAGAAAGGCTTTTAACTTATGCTGATATCAACATTTGCCCCACTAACTGGAAA
AGGATTGTTCTGGGAGCCACTCTTCTTGCCTCCAAGGTTTGGGATGATCAGGCTGTATGGAATGTGGACTACTGCCAGAT
CCTCAAGGACATTACAGTTGAGGACATGAATGAAATGGAAAGGCATTTTTTGGAGCTTCTTCAGTTTAATATTAATGCTC
CTGCCGGTGTTTATGCCAAACACTACCGTGACCTTCGCTCCTTAGCAGATGACAACAACCTGAATTTTCTATTTGCTCCT
GTTAGCAAAGAAAGAGCACAGAACCTAGCGGCTATTTCTAGATTATGTGAAGACAAAGACTTGTGTGGAGCAGCTATAAG
GTCTTTCAGCGCTGATAACTTCATTGGTATTCAGCACTCTAAAGCTATCCTCTCT

Alignment

ORF - retro_pabe_76 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 98.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLALESNPSDHPRASTIFLSKSQTDVREKRKSNHLNHVSPGQLTKKYSSCSTIFLDDSTVSQPNLRTTVK
          DL.LESNPSDHPRASTIFLSKSQT.VREKRKSNHLNH.S.GQLTKKYS.CSTIFLDD.TVSQPNLRTTVK
Retrocopy DLTLESNPSDHPRASTIFLSKSQTNVREKRKSNHLNHLSLGQLTKKYSLCSTIFLDDRTVSQPNLRTTVK

Parental  CVTLAIYYHIKNRDANRSLDIFDERSHPLTREKVPEEYFKHDPEHKFIYRFVRTLFSAAQLTAECAIVTL
          CVTL.IYYHIKNRDANRSLDIFDERSHPLTREKVP.EYFKHDPEHKFIYRFVRTLFSAAQLTAEC.IVTL
Retrocopy CVTLEIYYHIKNRDANRSLDIFDERSHPLTREKVPQEYFKHDPEHKFIYRFVRTLFSAAQLTAECPIVTL

Parental  VYLERLLTYAEIDICPTNWKRIVLGAILLASKVWDDQAVWNVDYCQILKDITVEDMNEMERHFLELLQFN
          VYLERLLTYA.I.ICPTNWKRIVLGA.LLASKVWDDQAVWNVDYCQILKDITVEDMNEMERHFLELLQFN
Retrocopy VYLERLLTYADINICPTNWKRIVLGATLLASKVWDDQAVWNVDYCQILKDITVEDMNEMERHFLELLQFN

Parental  INVPASVYAKYYFDLRSLADDNNLNFLFAPLSKERAQNLEAISRLCEDKDLCRAAMRRSFSADNFIGIQR
          IN.PA.VYAK.Y.DLRSLADDNNLNFLFAP.SKERAQNL.AISRLCEDKDLC.AA..RSFSADNFIGIQ.
Retrocopy INAPAGVYAKHYRDLRSLADDNNLNFLFAPVSKERAQNLAAISRLCEDKDLCGAAI-RSFSADNFIGIQH

Parental  SKAILS
          SKAILS
Retrocopy SKAILS

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	0.00 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_76 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_76 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_76 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 ,