RetrogeneDB ID: retro_ggor_1702

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2a:92388387..92389317(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GXYLT1
• Ensembl ID: ENSGGOG00000027928
• Aliases: None
• Description: None

Sequence

>retro_ggor_1702
GGTGAAAGACTGGAAGAAACAGTGACCATGTTGAAGTCAGCTATTATTTTCAGGATCAAACCTCTTCAATTCCAGATTTT
TGCTGAAGATCAACTACATCACAGCTTTAAAGGAAGGCTTGACAGGGGTCATTTCTACAAATATTTAATTATACAATATA
CTCCATAACCTTTCCAAGTGAGAATGCAGCAGAGTGGAAAAACTCTTTAAACCATGTGGTTTGCAGAGATTGTCCTTGCT
GTTATTCCTGAAAGAAGTTGACTCTCACACTGATAGCATTTTTAAAAGACCAGCTGATAATATTTGGTCTTTACTAAAGA
AATTTAATTCCACACAAATTCTGCAATGGCCCCAGAACACAAGGAACATCAAATAGGATGGTATAGTCGCTTTGCTAGGC
ATCCATACTGTGGAAAAGCTGGAGTAAACTCTGGAGTTATGTTGACAAACATGACTTGAATGAGAAGGAAGTATTTCAAG
AATAATATGACAACTGTGTGACTACAATGAGGAGATATACTTATGACATGGCTTAAAATGTACAAGTTAAACATTACATG
GGCGATCAAGATCTGTTGGATATCATGTTTTTTCATAATCCAGAAAACCTTTTTGTCTTTCCGTGTCAATGGAAGTGTCA
TCCAGATCATTGTCTATATGGAAGCAGTTGCCAAGAAGCAGAAGAAGGAATCTTTATTTTTCACGGGAACAGAGGTATTT
ACCATGATGATAAGCAACCAGCATTTAGAGCTGTTTATGAAGCACTGAGAAATTGTTCTTTTAAGATGACAATATTCATT
CATTAATAAAACCTTTAGAATTGGAACTACAAAAAACAGTGCATACATACCATGGAAAAATTTACTAAATATTTATCAAA
CAATTAGCAAAAACATAAGAGATCGCTATGTCAGATCACCAAAGGAAAGG

Alignment

ORF - retro_ggor_1702 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.19 %
• Parental protein coverage: 72.05 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GERLEETMTMLKSAIIFSIKPLQFHIFAEDQLHHSFKGRLDNW-SFLQTFNYTLYPITFPSENAAEWK-K
          GERLEET.TMLKSAIIF.IKPLQF.IFAEDQLHHSFKGRLD...SFLQ.FNYT.Y.ITFPSENAAEWK.K
Retrocopy GERLEETVTMLKSAIIFRIKPLQFQIFAEDQLHHSFKGRLDRG<SFLQIFNYTIYSITFPSENAAEWK<K

Parental  LFKPCASQRLFLPLILKEIDSLLYVDTDILFLRPVDDIWSLLKKFNSTQI-AAMAPEHEEPRIGWYNRFA
          LFKPC..QRL.L.L.LKE.DS.....TD..F.RP.D.IWSLLKKFNSTQI..AMAPEH.E..IGWY.RFA
Retrocopy LFKPCGLQRLSLLLFLKEVDS----HTDSIFKRPADNIWSLLKKFNSTQI<SAMAPEHKEHQIGWYSRFA

Parental  RHPYYGKTGVNSGVMLMNMTRMRRKYFKNDMTTVRLQWGDILMPLLKKYKLNITW-GDQDLLNIMFFHNP
          RHPY.GK.GVNSGVML.NMT.MRRKYFKN.MTTV.LQ.GDILM..LK.YKLNITW.GDQDLL.IMFFHNP
Retrocopy RHPYCGKAGVNSGVMLTNMT*MRRKYFKNNMTTV*LQ*GDILMTWLKMYKLNITW<GDQDLLDIMFFHNP

Parental  ESLFVFPCQWNYRPDHCIYGSNCQEAEEEGIFILHGNRGVYHDDKQPAFRAVYEALRNCSFE-DDNIRSL
          E.LFVFPCQW...PDHC.YGS.CQEA.EEGIFI.HGNRG.YHDDKQPAFRAVYEALRNCSF..DDNI.SL
Retrocopy ENLFVFPCQWKCHPDHCLYGSSCQEA-EEGIFIFHGNRGIYHDDKQPAFRAVYEALRNCSFK<DDNIHSL

Parental  LKPLELELQKTVHTYCGKIYKIFIKQLA-KSVRDRYARSPKEK
          .KPLELELQKTVHTY.GKIY.IFIKQLA.K..RDRY.RSPKE.
Retrocopy IKPLELELQKTVHTYHGKIY*IFIKQLA<KNIRDRYVRSPKER

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	1.05 RPM	0.72 RPM
SRP007412_cerebellum	0.32 RPM	1.26 RPM
SRP007412_heart	0.00 RPM	0.41 RPM
SRP007412_kidney	0.16 RPM	1.47 RPM
SRP007412_liver	0.03 RPM	1.64 RPM
SRP007412_testis	1.55 RPM	3.94 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_1702 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1702 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151233	5 retrocopies	retro_hsap_2295, retro_hsap_4167, retro_hsap_4177, retro_hsap_4258, retro_hsap_4267,
Gorilla gorilla	ENSGGOG00000027928	3 retrocopies	retro_ggor_1702 , retro_ggor_1950, retro_ggor_2798,
Monodelphis domestica	ENSMODG00000008913	1 retrocopy	retro_mdom_512,
Mus musculus	ENSMUSG00000036197	1 retrocopy	retro_mmus_2325,
Nomascus leucogenys	ENSNLEG00000017947	1 retrocopy	retro_nleu_2700,
Pongo abelii	ENSPPYG00000004419	2 retrocopies	retro_pabe_1849, retro_pabe_1976,
Pan troglodytes	ENSPTRG00000004836	5 retrocopies	retro_ptro_1623, retro_ptro_2832, retro_ptro_2960, retro_ptro_3006, retro_ptro_848,
Rattus norvegicus	ENSRNOG00000005234	1 retrocopy	retro_rnor_2754,