RetrogeneDB ID: retro_ggor_2119

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:127118302..127119310(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000008099
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NT5C3
• Ensembl ID: ENSGGOG00000028164
• Aliases: None
• Description: None

Sequence

>retro_ggor_2119
ATGAGGGCCCGGTCCATGGACCGCGCGGCCGTGGCGAGGGTGGGCGCGGTAGTGAGCGCCAGCGTGTGCGCCCTGGTGGC
GGGGGTGGTGCTGGCTCAGTACATATTCACCTTGAAGAGGAAGATGGGGCGGAAGACCAAGATCATCGAGATGATGCCAG
AATTCCAGAAAAGTTCAGTTCGAATCAAGAACCTTACAAGAGTAGAAGAAGTGATCTGTGGTCTTATCAAAGGAGGAGCT
GCCAAACTTCAGATAATAACAGACTTTGATATGACATTCAGTAGATTTTCATACAAAGGGAAAAGATGCCCAACATGTCA
TAATAGCATTGACAACTGTCAGCTGGTTACAGATGAATGTAGAAAAAAGTTATCGCAACTAAAGAAAAAATATTACGCTA
TTGAAGTTGATCCTGTTCTTACTGTAGAAGAGAAGTACCCTTATATGGTGGAATGGTATACTAAATCACATGGTTTGCTT
GGTCAACAAGCTTTACCAAAAGCTAAACTTAAAGAAATTGTGGCAGAATCTGACGTTATGCTCAAAGAAAGATATGAAGA
ATTTCTTTGATAAGCTCCAACAACATAGTATCCCCGTGTTCATATTTTCGGCTGGAATCGGCGATGTACTAGAGGAGGTT
ATTCGTCAAGCTGGTGTTTATCATCCAAATGTCAAAGTTGTGTCCAATTTTATGGATTTTGATGAAACTGGGGTGCGCAA
AGATTTAAAGGAGTTCTAATTCATATATTTAACAAACATGATGGTGCCTTGAGGAATACAGAATATTTCAATCAACTAAA
AGGCAATAGTAACATAATTCTTCTGGGAGCCTCCCAAGGAGACTTAAGAATGGCAGATGGAGTGGCCAATGTTGAGCACA
TTCTGAAAATTGGATATCTAAATGACAGAGTGGATGAGCTTTTAGAAAAGTACATGGACTCTTATGATATTGTTTTAGTA
CAAGATGAATCATTAGAAGTAGCCAACTCTATTTTACAGAAGATTCTA

Alignment

ORF - retro_ggor_2119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRAPSMDRAAVARVGAVASASVCALVAGVVLAQYIFTLKRKTGRKTKIIEMLSQKKKTSYRIYGLNRRQS
          MRA.SMDRAAVARVGAV.SASVCALVAGVVLAQYIFTLKRK.GRKTKIIEM.....K.S.RI..L.R...
Retrocopy MRARSMDRAAVARVGAVVSASVCALVAGVVLAQYIFTLKRKMGRKTKIIEMMPEFQKSSVRIKNLTRVEE

Parental  FLCGIMMNGMRKFNIITDFDMTLSRFSYKGKRCPTCHNIIDNCKLVTDECRKKLLQLKEKYYAIEVDPVL
          ..CG....G..K..IITDFDMT.SRFSYKGKRCPTCHN.IDNC.LVTDECRKKL.QLK.KYYAIEVDPVL
Retrocopy VICGLIKGGAAKLQIITDFDMTFSRFSYKGKRCPTCHNSIDNCQLVTDECRKKLSQLKKKYYAIEVDPVL

Parental  TVEEKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVMLKEGYE-NFFDKLQQHSIPVFIFSAGIGDV
          TVEEKYPYMVEWYTKSHGLL.QQALPKAKLKEIVAESDVMLKE.YE.NFFDKLQQHSIPVFIFSAGIGDV
Retrocopy TVEEKYPYMVEWYTKSHGLLGQQALPKAKLKEIVAESDVMLKERYE>NFFDKLQQHSIPVFIFSAGIGDV

Parental  LEEVIRQAGVYHPNVKVVSNFMDFDETGVLRG-FKGELIHVFNKHDGALRNTEYFNQLKDNSNIILLGDS
          LEEVIRQAGVYHPNVKVVSNFMDFDETGV....FKG.LIH.FNKHDGALRNTEYFNQLK.NSNIILLG.S
Retrocopy LEEVIRQAGVYHPNVKVVSNFMDFDETGVRKD<FKGVLIHIFNKHDGALRNTEYFNQLKGNSNIILLGAS

Parental  QGDLRMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVQDESLEVANSILQKIL
          QGDLRMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVQDESLEVANSILQKIL
Retrocopy QGDLRMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVQDESLEVANSILQKIL

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	0.86 RPM	4.36 RPM
SRP007412_cerebellum	0.63 RPM	6.19 RPM
SRP007412_heart	0.06 RPM	1.56 RPM
SRP007412_kidney	0.70 RPM	13.13 RPM
SRP007412_liver	0.40 RPM	9.23 RPM
SRP007412_testis	0.83 RPM	10.26 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_2119 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2119 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3084
Pan troglodytes	retro_ptro_2082

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006624	1 retrocopy	retro_amel_875,
Bos taurus	ENSBTAG00000016709	1 retrocopy	retro_btau_1465,
Canis familiaris	ENSCAFG00000003154	1 retrocopy	retro_cfam_1295,
Equus caballus	ENSECAG00000011777	1 retrocopy	retro_ecab_1118,
Homo sapiens	ENSG00000122643	1 retrocopy	retro_hsap_3084,
Gorilla gorilla	ENSGGOG00000028164	1 retrocopy	retro_ggor_2119 ,
Mustela putorius furo	ENSMPUG00000005546	2 retrocopies	retro_mputfur_1175, retro_mputfur_577,
Pteropus vampyrus	ENSPVAG00000013182	2 retrocopies	retro_pvam_148, retro_pvam_706,
Rattus norvegicus	ENSRNOG00000005981	1 retrocopy	retro_rnor_632,
Sus scrofa	ENSSSCG00000022912	1 retrocopy	retro_sscr_540,
Ictidomys tridecemlineatus	ENSSTOG00000026363	2 retrocopies	retro_itri_1325, retro_itri_682,