RetrogeneDB ID: retro_pabe_3192

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:148129130..148130362(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STRADB
• Ensembl ID: ENSPPYG00000013074
• Aliases: None
• Description: STE20-related kinase adaptor beta [Source:HGNC Symbol;Acc:13205]

Sequence

>retro_pabe_3192
AGTTCAAGAACACAAGTTGAATCACTCAAACATGAAAAACAAGTCTGAAACCAGTATCCATCAATACTTGGTCGATGAGC
CAACCCTTTCCTGGTCGCCTCCATCCACTAGAGCCAGTAAAGTAGTATGTTCCACCAACGTTTCTCACTGCAAGCTCCAA
GTAGAAATAAGAAGAGGATTTGACAACTTGACTTCTGTCCATCTTGCATGGCATACTCCTACGGGAACATTGGTAACTAT
AAAAATTACAAATCTGGAAAACTGCAATGAAGAATGCCTGAAAGTTTTACAGAAAGCCATGATTCTGTCCCACTTTTTCC
GGCATCCCAATATGACAACTTATTGGACAGTTTTCACTGTTGGCAGCTAGCTTTGGGTTATTTCTCCATTTATGGCCTAT
GGTTCAGCAAGTCAACTCTTGAGGACCTATTTTCCTGAAGGAATGAGTAAAACTTTAATAAGAACCATTCTCTTTGGAGC
AGTGAGAGGATTGAACTATCTCTACCAATATGGCTGTACTCACAGGAGAATTAAAGCCAGCCATATCCTCATTTCCGGTG
ATGGCCTAGTGACCCTCTCTGGCCTGTCCCATCTGCATAGTTTGGTTAAGCATGGACAGAGGCAGAGGGCGGTGTATGAT
TTCCCACAGTTCAGCATATCAGTGCAGCCGTGGCTGAGTCCAGAACTACTGAGACAGGATTTACATGGGTATAATGTGAA
GTCAGATATTTACAGTGTTGGGATTACAACATGTGAATTAGCCAGTGGGCAGGTGACTTTCCAGGACATGCATAGAACTC
AGATGCTGTTAACAGAAACTGAAAGGTCCCCCTTATAGCCCATTAGATATCAGTATTTTCCCTCAATCAGAATCCAAAAT
GAAAAATTCGTGGTCAGGTGTAGACTCTGGGATTGGAGCAAGTGTGCTTGTCTCCAGTGGAACTCACACAGTAAATAGTG
ACCGATTACACACACCATCCTCAAAAGCCTTCTCTCCTGCCTTCTTTAGCTGGGTACAGCTCTGTTTGCAACAAGATCCA
GAGAAAAGGCCATCAGCAAGCAGTTTATTGTCCCATGTTTTCTTCAAACAGATGAAAGAAGAAAGCCAGGATTCAATACT
TTCACTGTTGCCTCCTGCTTATAACAAGCCATCAATATCACTGCCTCCGGTGTTACCTTGGACTGAGCCAGAATGTGATT
TTCCTGATGAAAAAGACTCATATTGGGAATTC

Alignment

ORF - retro_pabe_3192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.48 %
• Parental protein coverage: 98.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TSRTQVESLRPEKQ-SETSIHQYLVDEPTLSWSPPSTRASEVLCSTNVSHYELQVEIGRGFDNLTSVHLA
          .SRTQVESL..EKQ.SETSIHQYLVDEPTLSWSPPSTRAS.V.CSTNVSH..LQVEI.RGFDNLTSVHLA
Retrocopy SSRTQVESLKHEKQ>SETSIHQYLVDEPTLSWSPPSTRASKVVCSTNVSHCKLQVEIRRGFDNLTSVHLA

Parental  RHTPTGTLVTIKITNLENCNEERLKALQKAVILSHFFRHPNITTYWTVFTVGSWLWVISPFMAYGSASQL
          .HTPTGTLVTIKITNLENCNEE.LK.LQKA.ILSHFFRHPN.TTYWTVFTVGS.LWVISPFMAYGSASQL
Retrocopy WHTPTGTLVTIKITNLENCNEECLKVLQKAMILSHFFRHPNMTTYWTVFTVGS*LWVISPFMAYGSASQL

Parental  LRTYFPEGMSETLIRNILFGAVRGLNYLHQNGCIHRSIKASHILISGDGLVTLSGLSHLHSLVKHGQRHR
          LRTYFPEGMS.TLIR.ILFGAVRGLNYL.Q.GC.HR.IKASHILISGDGLVTLSGLSHLHSLVKHGQR.R
Retrocopy LRTYFPEGMSKTLIRTILFGAVRGLNYLYQYGCTHRRIKASHILISGDGLVTLSGLSHLHSLVKHGQRQR

Parental  AVYDFPQFSTSVQPWLSPELLRQDLHGYNVKSDIYSVGITACELASGQVPFQDMHRTQMLL-QKLKGPPY
          AVYDFPQFS.SVQPWLSPELLRQDLHGYNVKSDIYSVGIT.CELASGQV.FQDMHRTQMLL.QKLKGPPY
Retrocopy AVYDFPQFSISVQPWLSPELLRQDLHGYNVKSDIYSVGITTCELASGQVTFQDMHRTQMLL>QKLKGPPY

Parental  SPLDISIFPQSESRMKNSRSGVDSGIGESVLVSSGTHTVNSDRLHTPSSKTFSPAFFSLVQLCLQQDPEK
          SPLDISIFPQSES.MKNS.SGVDSGIG.SVLVSSGTHTVNSDRLHTPSSK.FSPAFFS.VQLCLQQDPEK
Retrocopy SPLDISIFPQSESKMKNSWSGVDSGIGASVLVSSGTHTVNSDRLHTPSSKAFSPAFFSWVQLCLQQDPEK

Parental  RPSASSLLSHVFFKQMKEESQDSILSLLPPAYNKPSISLPPVLPWTEPECDFPDEKDSYWEF
          RPSASSLLSHVFFKQMKEESQDSILSLLPPAYNKPSISLPPVLPWTEPECDFPDEKDSYWEF
Retrocopy RPSASSLLSHVFFKQMKEESQDSILSLLPPAYNKPSISLPPVLPWTEPECDFPDEKDSYWEF

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	7.13 RPM
SRP007412_cerebellum	0.00 RPM	11.19 RPM
SRP007412_heart	0.06 RPM	40.79 RPM
SRP007412_kidney	0.30 RPM	57.58 RPM
SRP007412_liver	0.12 RPM	24.54 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3192 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3192 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3192 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3920
Gorilla gorilla	retro_ggor_2638
Macaca mulatta	retro_mmul_1741

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000082146	2 retrocopies	retro_hsap_147, retro_hsap_3920,
Gorilla gorilla	ENSGGOG00000012183	1 retrocopy	retro_ggor_2638,
Macaca mulatta	ENSMMUG00000018141	1 retrocopy	retro_mmul_1741,
Nomascus leucogenys	ENSNLEG00000006967	1 retrocopy	retro_nleu_2158,
Otolemur garnettii	ENSOGAG00000010744	1 retrocopy	retro_ogar_1019,
Pongo abelii	ENSPPYG00000013074	1 retrocopy	retro_pabe_3192 ,