RetrogeneDB ID: retro_ggor_2638

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:148957122..148958355(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STRADB
• Ensembl ID: ENSGGOG00000012183
• Aliases: None
• Description: None

Sequence

>retro_ggor_2638
AGTTCAAGAACACAAGTTGAATCACTCAAACATGAGAAACAAGTCTGAAACCAGTATCCATCAATACTTGGTCGAAGAGC
CAACCCTTTCCTGGTCGCCTCCATCCACTAGAGCCAGTGAAGTAGTACGTTCCGCCAACGTTTCTCACTGCGAGCTCCAA
GTAGAAATAGGAAGAGGATTTGACAAGTTGACTTCTGTCCATCTAGCACGGCATACTCCTACGGGAATGCTGGTAACTAC
AAAAATTACAAATCTGGAAAACGGCAATAAAGAATGCCTGAAAGTTTTACAGAAAGCCATGATTCTATCCCACTTTTTCC
GGCATCCCAATATTACAACTTATTGGACAGTTTTCACTGTTGGCAGTTGGCTTTGGGTTATTTCTCCATTTATGGCCTAT
GGTTCAGCAAGTCAACTCTTGAGGACCTATTTTCCTGAAGGAATGAGTAAAACTTTAATAAGAAACATTCTCTTTGGAGC
AGTGAGAGGATTGAACTATCTCTACCAATATGGCTGTATTCACAGGAGAATTAAAGCCAGCCATATCCTTATTTCTGGTG
ATGGCCTAGTGACCCTCTCTGGCCTGTCCCATCTGCATAGTTTGGTTAAGCATGGACAGAGGCATAGGGCTGTGTATGAT
TTCCCACAGTTCAGCACATTAGTGCAGCCATGGCTGAGTCCAGAACTACTGAGACAGGATTTACATGGGTATAATGTGAA
GTCAGATATTTACAGTGTTGGGATTACAACATGTGAATTAGCCAGTGGGCAGGTGCCTTTCCAGGACGTGCATAGAACTC
AGATGCTGTTAACAGAAACTGAAAGGTCCCCCTTATAGCCCATTGGATATCAGTATTTTCCCTCAATCAGAATCCAAAAT
GAAAAATTCCCGGTCAGGTGTAGACTCTGGGATTGGAGCAAGTGTGCTTGTCTCCAGTGGAACTCACACAGTAAATAGTG
ACCAATTACACACACCATCCTCAAAAACATTCTCTCCTGCCTTCTTTAGCTGGGTTACAGCTGTGTTTGCAACAAGATCC
AGAGAAAAGGCCATCAGCAAGCAGTTTATTGTCCCATGTTTTCTTCAAACAGATGAAAGAAGAAAGCCAGGATTCAATAC
TTTCACTGTTGCCTCCTGCTTATAACAAGCCATCAATATCACTGCCTCCGGTGTTACCTTGGACTGAGCCAGAATGTGGT
TTTCCTGATGAAAAAGATTCATATTGGGAATTC

Alignment

ORF - retro_ggor_2638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.49 %
• Parental protein coverage: 98.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TSRTQVESLRPEKQ-SETSIHQYLVDEPTLSWSPPSTRASEVLCSTNVSHYELQVEIGRGFDNLTSVHLA
          .SRTQVESL..EKQ.SETSIHQYLV.EPTLSWSPPSTRASEV..S.NVSH.ELQVEIGRGFD.LTSVHLA
Retrocopy SSRTQVESLKHEKQ>SETSIHQYLVEEPTLSWSPPSTRASEVVRSANVSHCELQVEIGRGFDKLTSVHLA

Parental  RHTPTGTLVTIKITNLENCNEERLKALQKAVILSHFFRHPNITTYWTVFTVGSWLWVISPFMAYGSASQL
          RHTPTG.LVT.KITNLEN.N.E.LK.LQKA.ILSHFFRHPNITTYWTVFTVGSWLWVISPFMAYGSASQL
Retrocopy RHTPTGMLVTTKITNLENGNKECLKVLQKAMILSHFFRHPNITTYWTVFTVGSWLWVISPFMAYGSASQL

Parental  LRTYFPEGMSETLIRNILFGAVRGLNYLHQNGCIHRSIKASHILISGDGLVTLSGLSHLHSLVKHGQRHR
          LRTYFPEGMS.TLIRNILFGAVRGLNYL.Q.GCIHR.IKASHILISGDGLVTLSGLSHLHSLVKHGQRHR
Retrocopy LRTYFPEGMSKTLIRNILFGAVRGLNYLYQYGCIHRRIKASHILISGDGLVTLSGLSHLHSLVKHGQRHR

Parental  AVYDFPQFSTSVQPWLSPELLRQDLHGYNVKSDIYSVGITACELASGQVPFQDMHRTQMLL-QKLKGPPY
          AVYDFPQFST.VQPWLSPELLRQDLHGYNVKSDIYSVGIT.CELASGQVPFQD.HRTQMLL.QKLKGPPY
Retrocopy AVYDFPQFSTLVQPWLSPELLRQDLHGYNVKSDIYSVGITTCELASGQVPFQDVHRTQMLL>QKLKGPPY

Parental  SPLDISIFPQSESRMKNSRSGVDSGIGESVLVSSGTHTVNSDRLHTPSSKTFSPAFFSLV-QLCLQQDPE
          SPLDISIFPQSES.MKNSRSGVDSGIG.SVLVSSGTHTVNSD.LHTPSSKTFSPAFFS.V.QLCLQQDPE
Retrocopy SPLDISIFPQSESKMKNSRSGVDSGIGASVLVSSGTHTVNSDQLHTPSSKTFSPAFFSWV>QLCLQQDPE

Parental  KRPSASSLLSHVFFKQMKEESQDSILSLLPPAYNKPSISLPPVLPWTEPECDFPDEKDSYWEF
          KRPSASSLLSHVFFKQMKEESQDSILSLLPPAYNKPSISLPPVLPWTEPEC.FPDEKDSYWEF
Retrocopy KRPSASSLLSHVFFKQMKEESQDSILSLLPPAYNKPSISLPPVLPWTEPECGFPDEKDSYWEF

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	8.44 RPM
SRP007412_cerebellum	0.04 RPM	8.67 RPM
SRP007412_heart	0.00 RPM	4.78 RPM
SRP007412_kidney	0.04 RPM	72.70 RPM
SRP007412_liver	0.11 RPM	61.57 RPM
SRP007412_testis	0.00 RPM	20.72 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2638 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2638 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3920
Pongo abelii	retro_pabe_3192
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,