RetrogeneDB ID: retro_ggor_2802

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:50113948..50115967(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DSE
• Ensembl ID: ENSGGOG00000026746
• Aliases: None
• Description: None

Sequence

>retro_ggor_2802
ATCAACCACGTTGGCCATCCGTGGCTTAAACAACACTTTGCATTTATGTATAGAACCATCCTGCCAGGGTTTCAAAGGAC
TGTGGCTATTGAGGACTCAAATTACAACTGATTTTATGGTCCAGAAAGCCAATTAGTGTTCCTTGATAAATTTATCATGC
GTAACAGCAGTGGTAACTGGCTAGCCGACCAAATCAGAAGGAACTGTGTGGTGGAAGGTCCAGGAACACTGTCCAAAGGG
CAGCGCCGGTGCACTCTGCACACAGAATTTCTCTGGTATGATGCCAGCTTGAAATCAGTTCCTCCTCCAGACTTTGGCAC
CCCTACGCTGCATTATTTTGAAGACTGGGTGTCGTGACTTGAAGTGCACTACCTGCTGAAATCAATAAATCTTTCCTCTC
TTTCAAGTGTGGAAAACTGGGGGGACATGCAATATGTGACATTGTCCACAGAAACAAATACAAAGATTGGAACAAAGGAT
GGAGAAATTTTAGGGCAGGGCATGAACATTATGATCAAAACTCATTTACTTTTGCTCCCAGTTGTGTGCCTTTCATTATT
GAGGCTCTGTACGGGCCAAAGTACACCTTTTCAACAATGTTTTGATGTTTTCCACAGCTGTGTCAAAGAGCTGCTTTTCT
CCCTGGAAGGGTCAAGTCACAGAAGACTGTTCATCAAAATGGTCTAAATACCAGCATGACCTGGCAGCTAGCTGTCAGGG
GAGAGTGGTTGCAGCAGAGGAGAAAAATGGGGTGGTTTTCATCTGAGGAGAAGGTGTGGGAGCTTATAACCCCCAGCTCA
ACCTGAAGAATGTTCAGAAGAATCTGATCCTCCTACATCCACAGCTGCTTCTCCTTGTAGACCAAATACACCTGGGAGAG
GAGAGTCCCCTGGAGACAGCAGCGAGCTTCTTCCACAATGTGGATGTTTCTTTTGAGGAGACTGTGGTAGATGGTATCCA
TGCGGCTTTCATCAGGTAGAGAAATTGTCTCTATAAAAACTACTGGATGGACAATACTGGCTACAGCAAGAAAGCAACAT
TTGCGTCAGTGACATATCCTGGGAGCTATCCCTACAATGGGACAAACTATGTGAATGTCACCATGCACCTCTGAAGTCCC
ATCACCGGGCCAGCTTACCTCTTCATAGGGTCACTATAGATGTTCAGAGCTTCACCATCCACGGAGACTCTCAGCAACGG
GATGTGTTCGTAGCCACCAGCGAACATGCCTAGGCAACGTACCTGTGGACAGGTGAGGCCGCAGGACAGTCTGCCTTTGC
ACAGGTCATTGCTGATCATCACAAAATTCTGTTTGACCAGAATTCAGCCATCAAGAGCAGCATTGTCCCTGAGGTGAAGG
ACTATGCTGCTATTGTGGAACAGAACCTGCAGCATTTTAAGCCAGTGTTTCAGCTGGAGAAGCAGATACTGTCCTGAGTC
CAGAACCAGCTAGCTTTAGGAAGACTGCTGACCGGCTGCTGAGATTTTCAGATAAGAGACAGGCTGAAGAGGCCATCGAC
AGGATTTTTGCCATAACACAGCAACAGCAGCAGCAAAACAAGTCAAAGAAAAACCAAAGGGCAGGCAAATGCTATAATTT
TGTGGATGCTGTCCCTGATATTTTTGCACAGATTGAGGTCAATGAGAAAAAGATTAGACAGAAAGCTCAGATTCAGGCAC
AGAAAGAACTACCCATAAATGAAGATGAAGAAATGAAAAACCTCTTAGATTTTGCAGATACAACATATGAGAAACATAAA
AATGGGGCTTGATGAAAGGCCGGGTTGGACAGGCATGGATGGTGACAACTACTCGTAGCAGGGCCTCATCACTATCTGCT
TCCTATACCAGATTGTTCCTCATCCTGAACATTGCTATTTTCTTTGTCATGTTGGCAATACAACTGACTTTTTCCAGAGG
GCCCAGAACCTACATGGCCAAAGATGTCTTTATGCAGTTCTTCTAATAGATAGCTGTATTTTATTGTGGTTGTACTCTTC
TTGTTCCCAATCACAGTGT

Alignment

ORF - retro_ggor_2802 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.58 %
• Parental protein coverage: 82.66 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  INHFGHPWLKQHFAFMYRTILPGFQRTVAIADSNYNWFYGPESQLVFLDKFVMRNGSGNWLADQIRRNRV
          INH.GHPWLKQHFAFMYRTILPGFQRTVAI.DSNYN.FYGPESQLVFLDKF.MRN.SGNWLADQIRRN.V
Retrocopy INHVGHPWLKQHFAFMYRTILPGFQRTVAIEDSNYN*FYGPESQLVFLDKFIMRNSSGNWLADQIRRNCV

Parental  VEGPGTPSKGQRWCTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW-GVVTYGSALPAEINRSFLSFKSG
          VEGPGT.SKGQR.CTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW.GVVT..SALPAEIN.SFLSFK.G
Retrocopy VEGPGTLSKGQRRCTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW<GVVT*-SALPAEINKSFLSFKCG

Parental  KLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTF-FNNVLMFSPA
          KLGG.AI.DIVHRNKYKDW.KGWRNF.AGHEH.DQNSFTFAP..VPFI.EALYGPKYTF.FNNVLMFS.A
Retrocopy KLGGHAICDIVHRNKYKDWNKGWRNFRAGHEHYDQNSFTFAPSCVPFIIEALYGPKYTF<FNNVLMFSTA

Parental  VSKSCFSPWVGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLI
          VSKSCFSPW.GQVTEDCSSKWSKY.HDLAASCQGRVVAAEEKNGVVFI.GEGVGAYNPQLNLKNVQ.NLI
Retrocopy VSKSCFSPWKGQVTEDCSSKWSKYQHDLAASCQGRVVAAEEKNGVVFI*GEGVGAYNPQLNLKNVQKNLI

Parental  LLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKAT
          LLHPQLLLLVDQIHLGEESPLETAASFFHNVDV.FEETVVDG.H.AFIR.R..LYK.YWMD.TGYS.KAT
Retrocopy LLHPQLLLLVDQIHLGEESPLETAASFFHNVDVSFEETVVDGIHAAFIR*RNCLYKNYWMDNTGYSKKAT

Parental  FASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGP-SIDVQSFTVHGDSQQLDVFIATSKHAYATYL
          FASVTYP..YPYNGTNYVNVTMHL.SPIT..AYLFIG...IDVQSFT.HGDSQQ.DVF.ATS.HA.ATYL
Retrocopy FASVTYPGSYPYNGTNYVNVTMHL*SPITGPAYLFIGS<TIDVQSFTIHGDSQQRDVFVATSEHA*ATYL

Parental  WTDEATGQSAFAQVIADRHKILFDRNSAIKSSIVPEVKDYAAIVEQNLQHFKPVFQLLEKQILSRVQN-T
          WT.EA.GQSAFAQVIAD.HKILFD.NSAIKSSIVPEVKDYAAIVEQNLQHFKPVFQ.LEKQILS.VQN..
Retrocopy WTGEAAGQSAFAQVIADHHKILFDQNSAIKSSIVPEVKDYAAIVEQNLQHFKPVFQ-LEKQILS*VQN<P

Parental  ASFRKTAERLLRFSDKRQTEEAIDRIFAISQQQQQQSKSKKNRRAGKRYKFVDAVPDIFAQIEVNEKKIR
          ASFRKTA.RLLRFSDKRQ.EEAIDRIFAI.QQQQQQ.KSKKN.RAGK.Y.FVDAVPDIFAQIEVNEKKIR
Retrocopy ASFRKTADRLLRFSDKRQAEEAIDRIFAITQQQQQQNKSKKNQRAGKCYNFVDAVPDIFAQIEVNEKKIR

Parental  QKAQILAQKELPIDEDEEMKDLLDFADVTYEKHKNG-GLIKGRFGQARMVTTTHSRAPSLSASYTRLFLI
          QKAQI.AQKELPI.EDEEMK.LLDFAD.TYEKHKNG.GL.KGR.GQA.MVTTT.SRA.SLSASYTRLFLI
Retrocopy QKAQIQAQKELPINEDEEMKNLLDFADTTYEKHKNG<GLMKGRVGQAWMVTTTRSRASSLSASYTRLFLI

Parental  LNIAIFFVMLAMQLT-YFQRAQSLHGQRCLYAVLLIDSCILLWLYSSCSQSQC
          LNIAIFFVMLA.QLT..FQRAQ.LHGQRCLYAVLLIDSCILLWLYSSCSQSQC
Retrocopy LNIAIFFVMLAIQLT<FFQRAQNLHGQRCLYAVLLIDSCILLWLYSSCSQSQC

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	3.50 RPM
SRP007412_cerebellum	0.00 RPM	4.45 RPM
SRP007412_heart	0.00 RPM	2.66 RPM
SRP007412_kidney	0.37 RPM	14.27 RPM
SRP007412_liver	0.00 RPM	16.12 RPM
SRP007412_testis	0.00 RPM	9.32 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_2802 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2802 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4178
Pan troglodytes	retro_ptro_2833
Pongo abelii	retro_pabe_3418

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013791	1 retrocopy	retro_acar_15,
Callithrix jacchus	ENSCJAG00000004530	1 retrocopy	retro_cjac_1174,
Homo sapiens	ENSG00000111817	1 retrocopy	retro_hsap_4178,
Gorilla gorilla	ENSGGOG00000026746	2 retrocopies	retro_ggor_1419, retro_ggor_2802 ,
Nomascus leucogenys	ENSNLEG00000013106	1 retrocopy	retro_nleu_2476,
Pongo abelii	ENSPPYG00000016948	2 retrocopies	retro_pabe_3418, retro_pabe_3517,
Pan troglodytes	ENSPTRG00000018529	1 retrocopy	retro_ptro_2833,
Sorex araneus	ENSSARG00000010799	1 retrocopy	retro_sara_560,
Takifugu rubripes	ENSTRUG00000006239	1 retrocopy	retro_trub_32,
Xenopus tropicalis	ENSXETG00000032776	1 retrocopy	retro_xtro_8,