RetrogeneDB ID: retro_ggor_31

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 21:24499190..24500345(+)
• Located in intron of: ENSGGOG00000026619

Retrocopy information

• Ensembl ID: ENSGGOG00000022623
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RIMKLB
• Ensembl ID: ENSGGOG00000000332
• Aliases: None
• Description: None

Sequence

>retro_ggor_31
ATCTGTAGTTCCGTGGCTGCCAAGTTGGGGTTTTTGACAGATTGTCCCATCAGGGAAGACTATCCTCAAACAGAGATCTT
ACGAGCACTGAAGGCCAAATGTTGTGAGGAGGAACTGGACTTTAGGGCTGTGGTGATGGATGAGGTGGTGCTGACAATGG
AGAAAGGAAACTTGGGTCTGCGGATCAATGGAGAGCTAATCACTGCCTACCCACAAGTGGTGGTAATCAGAGTACCAACC
CCTTGGGTGCAAAGTGATTGTGACATCACTGTTTTGCGCCATCTAGAGAAGATGGGATGCCAGTTAATGAACCGACCTCA
AGCCATCCTGAACTGCGTTAATAAGTTCTGGACATTTCAAGAGTTGGCTGGCCATGGTGTTCCTCTGCCAGATACTTTCT
CTTATGGTGGCCATGAAAATTTTGCTAAAATGATTGATGAAGCTCAAGTACTGGAGTTCCCAATGGTAGTAAAGAATATG
CGGGGTCATAGAGGTGAAGCCGTTTTCTTGGCTCGAGATAAGCACCATTTGGCTGATCTAAGCCATCTCATTTGCCATGA
AGCGCCATACTTGTTCCAGAAGTATGTTAAAGAGTCACATGGACGGGATGTACGTGTCATTGTCGTGGGAGGCCACATGG
TTGGCACCATGTTACATTGTTCAACAGATGGGAGAATGCAAAGCAACTGCTCATTAGGTGGTGTGGGGATGATGTGTTCA
TTGAGTGAACAAGGGAAGCAGCTAGCTATCCAGGTGTCTAATATCCTGGATGTGTGTGGCATTGACCTGTTGATGAAAGA
TGGCAGCTCCTTCTGTGTCTGTGAGGCCAATGCAAATGTAGATTTCATCGCCTTTGATAAGGCTTGTAATCTACATGTAG
CTGGTATCATAGCAGACTATACTGCCTCCCTTCTACCCCCTGGCCAGCTCACCCAGCGTATGTCCCTGCTCTCTGTGGTG
TCCACTGCCAGTGAGACTAGTGAGCCGGAGCTGGGTCCCCCAGCCAGCACTGCTGTTGACAACATAAGTGCAAGTTCCAG
CTCTGTTGACAGTGACCCTGAAAGCATAGAGCGAGAGCTGCTCACCAGACTCCCAGGGGGACTGTTCAACATGAACCAGC
TGCTAGCCAATGAAATCAAACTACTGGTGGACTGA

Alignment

ORF - retro_ggor_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCSSVAAKLWFLTDRRIREDYPQKEILRALKAKCCEEELDFRAVVMDEVVLTIEQGNLGLRINGELITAY
          .CSSVAAKL.FLTD..IREDYPQ.EILRALKAKCCEEELDFRAVVMDEVVLT.E.GNLGLRINGELITAY
Retrocopy ICSSVAAKLGFLTDCPIREDYPQTEILRALKAKCCEEELDFRAVVMDEVVLTMEKGNLGLRINGELITAY

Parental  PQVVVVRVPTPWVQSDSDITVLRHLEKMGCRLMNRPQAILNCVNKFWTFQELAGHGVPLPDTFSYGGHEN
          PQVVV.RVPTPWVQSD.DITVLRHLEKMGC.LMNRPQAILNCVNKFWTFQELAGHGVPLPDTFSYGGHEN
Retrocopy PQVVVIRVPTPWVQSDCDITVLRHLEKMGCQLMNRPQAILNCVNKFWTFQELAGHGVPLPDTFSYGGHEN

Parental  FAKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDKHHLADLSHLIRHEAPYLFQKYVKESHGRDVRVIVVG
          FAKMIDEA.VLEFPMVVKN.RGHRG.AVFLARDKHHLADLSHLI.HEAPYLFQKYVKESHGRDVRVIVVG
Retrocopy FAKMIDEAQVLEFPMVVKNMRGHRGEAVFLARDKHHLADLSHLICHEAPYLFQKYVKESHGRDVRVIVVG

Parental  GRVVGTMLRCSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQVSNILGMDVCGIDLLMKDDGSFCVCEANA
          G..VGTML.CSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQVSNIL..DVCGIDLLMKD..SFCVCEANA
Retrocopy GHMVGTMLHCSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQVSNIL--DVCGIDLLMKDGSSFCVCEANA

Parental  NVGFIAFDKACNLDVAGIIADYAASLLPSGRLTRRMSLLSVVSTASETSEPELGPPASTAVDNMSASSSS
          NV.FIAFDKACNL.VAGIIADY.ASLLP.G.LT.RMSLLSVVSTASETSEPELGPPASTAVDN.SASSSS
Retrocopy NVDFIAFDKACNLHVAGIIADYTASLLPPGQLTQRMSLLSVVSTASETSEPELGPPASTAVDNISASSSS

Parental  VDSDPESTERELLTKLPGGLFNMNQLLANEIKLLVD
          VDSDPES.ERELLT.LPGGLFNMNQLLANEIKLLVD
Retrocopy VDSDPESIERELLTRLPGGLFNMNQLLANEIKLLVD

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	0.48 RPM	35.20 RPM
SRP007412_cerebellum	0.16 RPM	36.96 RPM
SRP007412_heart	0.00 RPM	9.66 RPM
SRP007412_kidney	0.12 RPM	12.51 RPM
SRP007412_liver	0.11 RPM	3.48 RPM
SRP007412_testis	0.21 RPM	80.19 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_31 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_31 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2506
Pan troglodytes	retro_ptro_1457
Pongo abelii	retro_pabe_1844

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000166532	1 retrocopy	retro_hsap_2506,
Gorilla gorilla	ENSGGOG00000000332	1 retrocopy	retro_ggor_31 ,
Nomascus leucogenys	ENSNLEG00000002201	2 retrocopies	retro_nleu_1422, retro_nleu_1437,
Oryctolagus cuniculus	ENSOCUG00000013997	1 retrocopy	retro_ocun_1777,
Otolemur garnettii	ENSOGAG00000011440	2 retrocopies	retro_ogar_1183, retro_ogar_2985,
Pongo abelii	ENSPPYG00000004244	1 retrocopy	retro_pabe_1844,
Pan troglodytes	ENSPTRG00000004643	1 retrocopy	retro_ptro_1457,
Rattus norvegicus	ENSRNOG00000023814	1 retrocopy	retro_rnor_255,
Tarsius syrichta	ENSTSYG00000003996	1 retrocopy	retro_tsyr_1977,
Tursiops truncatus	ENSTTRG00000000699	3 retrocopies	retro_ttru_1672, retro_ttru_366, retro_ttru_460,
Vicugna pacos	ENSVPAG00000003954	1 retrocopy	retro_vpac_256,