RetrogeneDB ID: retro_pabe_1493

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:30167430..30168324(-)
• 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_1493
ATGGAGTCGCAGAAAGAGGCGCGAACACTCCAGGAACCCATCGCGCGGCCGCCTGGGGCCTCAAGGTCTCAGACGCCAAA
ATACAAGGAGCGGCGGGAGGGCGGCGCGGTGCTGGCGACGGCTGCCCTGGGCGCAGAGGTGGACGACGCTAGTGTGGACG
AGCTGTGGCTGCTGCAGGTGGAGCCGGCCGAGCTGAGGCCTGAGTGCAGCCGCTGCAGCCGGCCTCAGAAAGTGTGTTTG
TGTCCATTTCTCCCAGCGCACCCTTTGCATATCTCTACCCACTTGTACATAATTCAGCATCCAGCAGAGGAACACAAAAT
GTTGCGGACAGTTCCTCTACCAGCAGCATGCCTCCCCCAAGACAAGTGCAAAGCGAAGACTGGTCGTCGCTTCAGTGAAG
AAAGAGATCCTGAACTTTCAACTGTTTGCCGGAAGTTTGGTACATTAATATTATATCCAGGGGCTGAAGCTGCTAATCTG
GAAGAATTTATATTAGATTCTCCTGTTTATCCTCTACAATCATCATCATTGATGGTACACGGAGCCAGGCTAAAGACATT
TTCTGTAAGAATTCCTTGTTCTGACACCCCCAAACAGGTGCAGTTAAAAATTAGCATTTCTAGTCAGTATGTAGTTCAGA
TGCAGCCAATTAATAGATGTCTTTCTACACTGGAGTGTGCACCTGTTGCTCTTTCCATCTTGGAGAAAAATAATTACATA
CAAGAGACTTTGCTCCGCCCTCTTGAAGCTTTATGCTCTTTCCAGGTTTAACATGGTGACCAAATTCGCCTCAGCAAGGA
ACACCTTCTGAAAAATGGATTATATCCTAAACCAATGCCAAAGAACAAACACAAACTCAGGAAAATGGAACTATTAAAGA
ATAGTGTTAAAATT

Alignment

ORF - retro_pabe_1493 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MESQKEARTFQEPVARPPGTSRSQTPNDKERREGGAVPAATALGAEADDDSADGLWELPVEPAERRPECT
          MESQKEART.QEP.ARPPG.SRSQTP..KERREGGAV.A..ALGAE.DD.S.D.LW.L.VEPAE.RPEC.
Retrocopy MESQKEARTLQEPIARPPGASRSQTPKYKERREGGAVLATAALGAEVDDASVDELWLLQVEPAELRPECS

Parental  RCSRPQKVCLCPFLPAHPLHISTHLYIIQHPAEENKVLRTVPLLAACLPQDKCKVKIGRRFSEERDPELS
          RCSRPQKVCLCPFLPAHPLHISTHLYIIQHPAEE.K.LRTVPL.AACLPQDKCK.K.GRRFSEERDPELS
Retrocopy RCSRPQKVCLCPFLPAHPLHISTHLYIIQHPAEEHKMLRTVPLPAACLPQDKCKAKTGRRFSEERDPELS

Parental  SVCRKSGTLILYPGAEAANLEEFILDSPVYP-STIIIIDGTWSQAKDIFYKNSLFRH-PKQVQLKTSISS
          .VCRK.GTLILYPGAEAANLEEFILDSPVYP.STIIIIDGT.SQAKDIF.KNSLF.H.PKQVQLK.SISS
Retrocopy TVCRKFGTLILYPGAEAANLEEFILDSPVYP<STIIIIDGTRSQAKDIFCKNSLF*H>PKQVQLKISISS

Parental  QYVIRMQPTNRCLSTLECAAVALSILEKNNYIQETLLRPLQALCSFQLQHGAQIRLSKEHLLKNGLYPKP
          QYV..MQP.NRCLSTLECA.VALSILEKNNYIQETLLRPL.ALCSFQ..HG.QIRLSKEHLLKNGLYPKP
Retrocopy QYVVQMQPINRCLSTLECAPVALSILEKNNYIQETLLRPLEALCSFQV*HGDQIRLSKEHLLKNGLYPKP

Parental  MPKNKRKLRKMELLMNSVKI
          MPKNK.KLRKMELL.NSVKI
Retrocopy MPKNKHKLRKMELLKNSVKI

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	0.22 RPM	0.50 RPM
SRP007412_cerebellum	0.00 RPM	1.34 RPM
SRP007412_heart	0.21 RPM	0.84 RPM
SRP007412_kidney	0.43 RPM	0.63 RPM
SRP007412_liver	0.24 RPM	0.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1493 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1493 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1493 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,