RetrogeneDB ID: retro_pabe_609

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:72500108..72500809(-)
• Located in intron of: ENSPPYG00000002410

Retrocopy information

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

Parental gene information

• Parental gene symbol: TATDN1
• Ensembl ID: ENSPPYG00000018868
• Aliases: None
• Description: TatD DNase domain containing 1 [Source:HGNC Symbol;Acc:24220]

Sequence

>retro_pabe_609
AAACAAATCATATGTTTTTTCAGCACAGTTGGATGTCATCCTACAAGATGTGGTGAATTTGAAAAGAATAACCCTGATCT
TTACTTAAAGAGTGCTAAATCTTGCTGAAAACAATAAAGGGGAAAGTTGTGGCAATAGGAGAATGTGGACTTGATTTTGA
CTGAACCTGCAGTTTTGTCCCAAAGATACTCAACTCGAAATATTGTGAAAAACAGTTTGAACTGTCAGAACAAACAAAAT
TACCAATGTTTCTTCATTGTCGAAACTCACATGCTGAATTTTTGGACATAATTAAAAGAAATAGAGATCGGTGTGTAGGG
GGAGTGGTGCACTCATTTGATGGTACCAAGGAAGCAGCAGCTGCTTTGATTGACTTGGATCTTTATATAGGATTTAATGG
TTGCTCACTGAAAACTGAAACTAATTTGGAAGTTCTGAAGTCAATTCCTAGTGAAAAATTAATGATTGAGACAAATGCAC
CTTGGTGTGGAGTCAAAAGTACACATGCTGGATCAAAATATATAAAAACTGCATTTCCTACCAAAAAGAAGTGGGAAAGT
GGGCACTGCTTAAAAGACATAAATGAACTCTGCCATGTAATTCAAATATTGGAGATAACGTCAGCAGTGAGAGACGAGGA
TCCACTGGAATCAGCCAATACACTATATAACAATACTATGAAAGTATTTTTTCCTGGAATA

Alignment

ORF - retro_pabe_609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.38 %
• Parental protein coverage: 98.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KFIDMFFSTVGCHPTRCGEFEKNNPDLYLKELLN-LAENNKGKVVAIGECGLDFD-RLQFCPKDTQLKYF
          K.I..FFSTVGCHPTRCGEFEKNNPDLYLK.....L....KGKVVAIGECGLDFD....F.PK....KY.
Retrocopy KQIICFFSTVGCHPTRCGEFEKNNPDLYLKSAKS<LLKTIKGKVVAIGECGLDFD*TCSFVPKILNSKYC

Parental  EKQFELSEQTKLPMFLHCRNSHAEFLDIMKRNRDRCVGGVVHSFDGSKEAAAALIDLDLYIGFNGCSLKT
          EKQFELSEQTKLPMFLHCRNSHAEFLDI.KRNRDRCVGGVVHSFDG.KEAAAALIDLDLYIGFNGCSLKT
Retrocopy EKQFELSEQTKLPMFLHCRNSHAEFLDIIKRNRDRCVGGVVHSFDGTKEAAAALIDLDLYIGFNGCSLKT

Parental  EANLEVLKSIPSEKLMIETDAPWCGVKSTHAGSKYIKTAFPTKKKWESGHCLKDRNEPCHIIQILEIMSA
          E.NLEVLKSIPSEKLMIET.APWCGVKSTHAGSKYIKTAFPTKKKWESGHCLKD.NE.CH.IQILEI.SA
Retrocopy ETNLEVLKSIPSEKLMIETNAPWCGVKSTHAGSKYIKTAFPTKKKWESGHCLKDINELCHVIQILEITSA

Parental  VRDEDPLELANTLYNNTIKVFFPGI
          VRDEDPLE.ANTLYNNT.KVFFPGI
Retrocopy VRDEDPLESANTLYNNTMKVFFPGI

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	1.38 RPM	6.52 RPM
SRP007412_cerebellum	2.07 RPM	8.03 RPM
SRP007412_heart	1.17 RPM	3.64 RPM
SRP007412_kidney	0.96 RPM	5.60 RPM
SRP007412_liver	0.43 RPM	2.26 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_609 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_609 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_609 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_578
Gorilla gorilla	retro_ggor_514

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000018868	1 retrocopy	retro_pabe_609 ,
Tarsius syrichta	ENSTSYG00000001819	1 retrocopy	retro_tsyr_1479,