RetrogeneDB ID: retro_ggor_398

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:67119392..67120873(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000025825
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC2A3
• Ensembl ID: ENSGGOG00000016813
• Aliases: None
• Description: None

Sequence

>retro_ggor_398
GGGACATAGAAGGTCACCCCATCTCTGATCTTCGCCATCACAATTGCTACAATCGGCTCTTTCCAATTTGGCTACAACAC
TGGGGTCATCAATGCTCCTGAGATGATCGTAAGGGAATTTATCAACACTTTGATGGACAAGGCAAATACCCCTCCCTCTG
AGATGTTGCGCTTGTCCCTTTGGTGCTTGTCTATGGCCATATTCTCCATTGGTTGTATGACTGGCTTCTTTTCTGTTGGA
CTGTTTGTCAACAGCTTTGACAGGCATAATTCAATGCTTACGGTCAACCTGTTGGCTGTCACTGGTGGCTGCCTTATGGG
ATTGTGTAAAGTAGCTGAGTTGGTTGAAATACTGATCCTGGCCTACTTGGTTATTGGCCTCTTCTGCAGACTCTGCACAG
GTTTTGTGCCCACGTACATCGGAGACATCTCACCTATTGCCCTGCAAGGTGTCTTTGGCACTCTCAACCAGCTGGGCATT
GTTATTGGAATTCTGGTGGCCCAGATCTTTGATCTGGAATTCATCCTGGGGTCCGAAGACCTATGGCCTGTGCTATTAGG
CTTTCCCATCTCTCCTGCTATGCTACAAAGTGCAGCCCTTCCTTTTTGTCCTGAAAGTCCCAGATTCTTGCTCATTAACA
GAAAAGAAGAGGAGAATGCTAAGGAGATCCTCCAGTGGTTGTGGGGCACCCAGGATGTATCCCAAGACATCCAGGAGATG
AAAGATGAGAGTGCAAGGATGGCACAAGAAAAGCAAGTCACTGTGCTGGAGCTCTTTAGAGTATCCAGCTACCGACAGCC
CATCATCATTTCCATCATGCTCCAGCTCTCTCAGCAGCTCTCTGGAATCAATACTGTGTTCTATTACTCAACAGGAATCT
TTAAGGGTACAGGTGTTCAAGAGCCCATCTGTGTCACCATTGGTGCGGGTGTGGTTAATACTGTCTTCACTATAGTTTCC
CTATTTCTAGTGGAAAGGGAAGTAAGAAGGACTCTACATATGATAGGCCTTGGAGGGATGGCTTTTTGTTCTATCCTCAT
GACTGTTTGTTTGTTATTGAAGGATGAGTGTAATGGGATAAGCTTTGTCTGTATTGGGGCTATCTTGGTCTTTGTGGTCT
TCTTTGAAATTGGGCCAGACCACATTCCCTGGTTTATTGTGGCTGAACTCTTCAGCCAGGGCCCTGGCCCAGCTGTGATG
GCAGTGGCCGGCTGTTTCAACTGGACCTCCAACTTCCTAGTCAGATTGCTTTTCCCTTCTGCTGCTTACTATTTAGGAGC
CTACGTTTTTATTATCTTCACCGACTTCCTCATTACCTTCTTGATCTTTACCTTCTTCAAAGTCCCTGAGATGTGTTACA
GGACTTTCGAAGATATCACACAGGCCTTTGAGGGGCAGGCACACGATGCAAATAGATCTGGAAGTCCTGCGTCATGGAGA
TGAACAGTATCCAGCCTGCTAAGGAGACCACCACCAATGTC

Alignment

ORF - retro_ggor_398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.87 %
• Parental protein coverage: 99.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GTQKVTPALIFAITVATIGSFQFGYNTGVINAPEKIIKEFINKTLTDKGNAPPSEVLLTSLWSLSVAIFS
          GT.KVTP.LIFAIT.ATIGSFQFGYNTGVINAPE.I..EFIN.TL.DK.N.PPSE.L..SLW.LS.AIFS
Retrocopy GT*KVTPSLIFAITIATIGSFQFGYNTGVINAPEMIVREFIN-TLMDKANTPPSEMLRLSLWCLSMAIFS

Parental  VGGMIGSFSVGLFVNRFGRRNSMLIVNLLAVTGGCFMGLCKVAKSVEMLILGRLVIGLFCGLCTGFVPMY
          .G.M.G.FSVGLFVN.F.R.NSML.VNLLAVTGGC.MGLCKVA..VE.LIL..LVIGLFC.LCTGFVP.Y
Retrocopy IGCMTGFFSVGLFVNSFDRHNSMLTVNLLAVTGGCLMGLCKVAELVEILILAYLVIGLFCRLCTGFVPTY

Parental  IGEISPTALRGAFGTLNQLGIVIGILVAQIFGLELILGSEELWPLLLGFTILPAILQSAALPFCPESPRF
          IG.ISP.AL.G.FGTLNQLGIVIGILVAQIF.LE.ILGSE.LWP.LLGF.I.PA.LQSAALPFCPESPRF
Retrocopy IGDISPIALQGVFGTLNQLGIVIGILVAQIFDLEFILGSEDLWPVLLGFPISPAMLQSAALPFCPESPRF

Parental  LLINRKEEENAKQILQRLWGTQDVSQDIQEMKDESARMSQEKQVTVLELFRVSSYRQPIIISIVLQLSQQ
          LLINRKEEENAK.ILQ.LWGTQDVSQDIQEMKDESARM.QEKQVTVLELFRVSSYRQPIIISI.LQLSQQ
Retrocopy LLINRKEEENAKEILQWLWGTQDVSQDIQEMKDESARMAQEKQVTVLELFRVSSYRQPIIISIMLQLSQQ

Parental  LSGINAVFYYSTGIFKDAGVQEPIYATIGAGVVNTIFTVVSLFLVERAGRRTLHMIGLGGMAFCSTLMTI
          LSGIN.VFYYSTGIFK..GVQEPI..TIGAGVVNT.FT.VSLFLVER..RRTLHMIGLGGMAFCS.LMT.
Retrocopy LSGINTVFYYSTGIFKGTGVQEPICVTIGAGVVNTVFTIVSLFLVEREVRRTLHMIGLGGMAFCSILMTV

Parental  SLLLKDNYNGMSFVCIGAILVFVAFFEIGPGPIPWFIVAELFSQGPRPAAMAVAGCSNWTSNFLVGLLFP
          .LLLKD..NG.SFVCIGAILVFV.FFEIGP..IPWFIVAELFSQGP.PA.MAVAGC.NWTSNFLV.LLFP
Retrocopy CLLLKDECNGISFVCIGAILVFVVFFEIGPDHIPWFIVAELFSQGPGPAVMAVAGCFNWTSNFLVRLLFP

Parental  SAAYYLGAYVFIIFTGFLITFLAFTFFKVPETRGRTFEDITRAFEGQAHGADRSG-KDGVMEMNSIEPAK
          SAAYYLGAYVFIIFT.FLITFL.FTFFKVPE...RTFEDIT.AFEGQAH.A.RSG.K..VMEMNSI.PAK
Retrocopy SAAYYLGAYVFIIFTDFLITFLIFTFFKVPEMCYRTFEDITQAFEGQAHDANRSG<KSCVMEMNSIQPAK

Parental  ETTTNV
          ETTTNV
Retrocopy ETTTNV

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	0.14 RPM	44.17 RPM
SRP007412_cerebellum	0.24 RPM	30.93 RPM
SRP007412_heart	0.03 RPM	7.38 RPM
SRP007412_kidney	0.29 RPM	19.54 RPM
SRP007412_liver	0.18 RPM	26.64 RPM
SRP007412_testis	0.93 RPM	229.99 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_398 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_398 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_401
Pan troglodytes	retro_ptro_307
Pongo abelii	retro_pabe_315
Macaca mulatta	retro_mmul_502

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004556	2 retrocopies	retro_btau_708, retro_btau_709,
Callithrix jacchus	ENSCJAG00000018988	1 retrocopy	retro_cjac_446,
Cavia porcellus	ENSCPOG00000003074	1 retrocopy	retro_cpor_761,
Cavia porcellus	ENSCPOG00000009834	1 retrocopy	retro_cpor_760,
Cavia porcellus	ENSCPOG00000011295	1 retrocopy	retro_cpor_587,
Felis catus	ENSFCAG00000001625	1 retrocopy	retro_fcat_1924,
Homo sapiens	ENSG00000059804	2 retrocopies	retro_hsap_3983, retro_hsap_401,
Gorilla gorilla	ENSGGOG00000016813	1 retrocopy	retro_ggor_398 ,
Macaca mulatta	ENSMMUG00000000439	2 retrocopies	retro_mmul_2301, retro_mmul_502,
Nomascus leucogenys	ENSNLEG00000026903	2 retrocopies	retro_nleu_1572, retro_nleu_1904,
Oryctolagus cuniculus	ENSOCUG00000008575	1 retrocopy	retro_ocun_352,
Pongo abelii	ENSPPYG00000004235	1 retrocopy	retro_pabe_315,
Pan troglodytes	ENSPTRG00000004626	1 retrocopy	retro_ptro_307,