RetrogeneDB ID: retro_pabe_1494

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:30172586..30173144(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DTWD2
• Ensembl ID: ENSPPYG00000015707
• Aliases: None
• Description: DTW domain containing 2 [Source:HGNC Symbol;Acc:19334]

Sequence

>retro_pabe_1494
TTGCCAGCAGCATGCCTCCCCCAAGACAAGTGCAAAGCGAAGACTGGTCGTCGCTTCAATGAAGAAAGAGATCCTGAACT
TTCAACTGTTTGCCGGAAGTTTGGTACATTAATATTATATCCAGGGGCTGAAGCTGCTAATCTGGAAGAATTTATATTAG
ATTCTCCTGTTTATCCTCTACAATCATCATCATTGATGGTACACGGAGCCAGGCTAAAGACATTTTTTGTAAGAATTCCT
TGTTCTGACACCCCCAAACAGGTGCAGTTAAAAATTAGCATTTCTAGTCAGTATGTAGTTCAGATGCAGCCAATTAATAG
ATGTCTTTCTACACTGGAGTGTGCACCTGTTGCTCTTTCCATCTTGGAGAAAAATAATTACATACAAGAGACTTTGCTTC
GCCCTCTTAAAGCTTTATGCTCTTTCCAGGTTTAACATGGTGACCAAATCCGCCTCAGCAAGGAACACCTTCTGAAAAAT
GGATTATATCCTAAACCAATGCCAAAGAACAAACACAAACTCAGGAAAATGGAACTATTAAAGAATAGTGTTAAAATT

Alignment

ORF - retro_pabe_1494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.3 %
• Parental protein coverage: 62.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLAACLPQDKCKVKIGRRFSEERDPELSSVCRKSGTLILYPGAEAANLEEFILDSPVYP-STIIIIDGTW
          L.AACLPQDKCK.K.GRRF.EERDPELS.VCRK.GTLILYPGAEAANLEEFILDSPVYP.STIIIIDGT.
Retrocopy LPAACLPQDKCKAKTGRRFNEERDPELSTVCRKFGTLILYPGAEAANLEEFILDSPVYP<STIIIIDGTR

Parental  SQAKDIFYKNSLFRH-PKQVQLKTSISSQYVIRMQPTNRCLSTLECAAVALSILEKNNYIQETLLRPLQA
          SQAKDIF.KNSLF.H.PKQVQLK.SISSQYV..MQP.NRCLSTLECA.VALSILEKNNYIQETLLRPL.A
Retrocopy SQAKDIFCKNSLF*H>PKQVQLKISISSQYVVQMQPINRCLSTLECAPVALSILEKNNYIQETLLRPLKA

Parental  LCSFQLQHGAQIRLSKEHLLKNGLYPKPMPKNKRKLRKMELLMNSVKI
          LCSFQ..HG.QIRLSKEHLLKNGLYPKPMPKNK.KLRKMELL.NSVKI
Retrocopy LCSFQV*HGDQIRLSKEHLLKNGLYPKPMPKNKHKLRKMELLKNSVKI

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	0.06 RPM	0.50 RPM
SRP007412_cerebellum	0.00 RPM	1.34 RPM
SRP007412_heart	0.15 RPM	0.84 RPM
SRP007412_kidney	0.23 RPM	0.63 RPM
SRP007412_liver	0.12 RPM	0.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1494 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1494 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1494 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014789	1 retrocopy	retro_dnov_2188,
Gorilla gorilla	ENSGGOG00000009599	1 retrocopy	retro_ggor_2167,
Pongo abelii	ENSPPYG00000015707	2 retrocopies	retro_pabe_1493, retro_pabe_1494 ,
Pan troglodytes	ENSPTRG00000017164	1 retrocopy	retro_ptro_1168,