RetrogeneDB ID: retro_ggor_1158

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 15:46021360..46022678(+)
• Located in intron of: ENSGGOG00000013002

Retrocopy information

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

Parental gene information

• Parental gene symbol: LETM1
• Ensembl ID: ENSGGOG00000002923
• Aliases: None
• Description: None

Sequence

>retro_ggor_1158
TTTTCCAGAAGATCTGAGAGACAGGAAAGACCTAACAATGAAGAAATCATGCGCTTTCCCAAATTATTTGAGGATGAGCT
GACCCTGGATAACCTCACCTGCCAGCAGCTGGTGGCATTGTGTGAGCTGCTGGGTCTCCAGGCCATAGGCACCAACAACT
TCCTATGCTTCCAGCTCACCATGAGGTTGAGGTCCATAAAGGCCAACAATGAGTTGATTGCTGAGGAAGGGGTGGACAGC
CTGAATATCAAGGAATTGCTGTCGACATGTAGAACTCGAGGGATGTGGGCCCTCAGGGTCTCAGAAAACCATCTGAGGAG
CCTGCTGAAGCAGTGGCTGGACCTGCATTTGCATCAAGAGATCCCCATATCACTGCTCTTATTGTCCTGAGCTATGTACC
TCCCAGACACCCTCTCTCCTACTGACCAGCTCAAATCCACCTTGCCGACTCTTCCAGAGACAGTGGTGAAGGGAGCCCAG
GTGAAAGTGGACAAGGTTGAGGGTGAGCAGGTGGACAACAAAGTGAAATTGGAGGCCACATTACAGGAGGAGACGGCCAT
CCAGCTGGAGCACAGGGAGAATGAGCTGCAGAAGCTATCCCAAGAAACGAAGTGGAAGAAGCCACCCCTGAGAGGCCAGT
GGCTGACCAGCAGCCAGAAGTGCCTGATGTGATCCTGCCCTCAGAGGCCCTGAAGGACACTGCCCCTGTGCTGGAGATCT
TGAAGGAGGAGAAAATAACTAAAGAAGAAATGGGTGTACTTAGCGATGCATGTTCTAAACTGAAGGAGCAAAATAAGTCC
CTAACCAAGGAGAAGGAGGAGCTGGAGCTGCTGAAGGAGGATGTCCAGGACGATAGTGATGACTTGCAAGAGATCAAGAA
GGAAGTTTCAAAGACCAGCAAAGAAAAATATGTGGAAAAATCTAAAGCCAGCAAGACACTGACAAAGAGAGTTCAGCAGA
TGATCTGGCGGATAGACAGCTTGATTGCACAGCTGGAGATGGATCAGAGGCCTGGCAAGCTGGGCCAGGCAGAGAGCTCA
GGGGGAGTGGGAGAGAAAGTCATCAGTATCACTGAGCTCATCAGCGCCATGAAGCAAATCAAGAACATTCCAGAAAACAA
GCTGATCAGCTTGGCCTCAACACTGGATAAAAGTAAGAATGGCAAGGTCAACATTGACAAGCTCATTAAGGTGATTGAGC
TTGTGGACAAAGATGTTCACGTCTCTACCAGTCAGGTGGCTGAGATGGTAGCAATGCTGGAGAAGGAGGAGAGGTGGAGG
AGAAGAAGAAGGCTAAGGGAAAGGCTGAGGAGGAGGCT

Alignment

ORF - retro_ggor_1158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.78 %
• Parental protein coverage: 59.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FQKIRETGERPSNEEIMRFSKLFEDELTLDNLTRPQLVALCKLLELQSIGTNNFLRFQLTMRLRSIKADD
          F....E..ERP.NEEIMRF.KLFEDELTLDNLT..QLVALC.LL.LQ.IGTNNFL.FQLTMRLRSIKA..
Retrocopy FSRRSERQERPNNEEIMRFPKLFEDELTLDNLTCQQLVALCELLGLQAIGTNNFLCFQLTMRLRSIKANN

Parental  KLIAEEGVDSLNVKELQAACRARGMRALGVTEDRLRGQLKQWLDLHLHQEIPTSLLILSRAMYLPDTLSP
          .LIAEEGVDSLN.KEL...CR.RGM.AL.V.E..LR..LKQWLDLHLHQEIP.SLL.LS.AMYLPDTLSP
Retrocopy ELIAEEGVDSLNIKELLSTCRTRGMWALRVSENHLRSLLKQWLDLHLHQEIPISLLLLS*AMYLPDTLSP

Parental  ADQLKSTLQTLPEIVAKEAQVKVAEVEGEQVDNKAKLEATLQEEAAIQQEHREKELQKRS-EAAKDVEPE
          .DQLKS...TLP.....E..VK.A.V....V............EA..Q.E.....L..R..E.A....P.
Retrocopy TDQLKS---TLPTL--PETVVKGAQVKVDKVEGE-QVDNKVKLEATLQ-EETAIQLEHRE<E*AAEAIPR

Parental  RVV--AAPQRPGTEPQPEMPDTVLQSETLKDTAPVLEGLKEEEITKEEIDILSNACSKLQEQKKSLTKEK
          ..V..A.P.RP....QPE.PD..L.SE.LKDTAPVLE.LKEE.ITKEE...LS.ACSKL.EQ.KSLTKEK
Retrocopy NEVEEATPERPVADQQPEVPDVILPSEALKDTAPVLEILKEEKITKEEMGVLSDACSKLKEQNKSLTKEK

Parental  EELEPLKEDVQDYSEDLQEIKKELSKTGEEKYVEESKASKRLTKRVQQMIGQIDGLISQLEMDQQAGKLA
          EELE.LKEDVQD.S.DLQEIKKE.SKT..EKYVE.SKASK.LTKRVQQMI..ID.LI.QLEMDQ..GKL.
Retrocopy EELELLKEDVQDDSDDLQEIKKEVSKTSKEKYVEKSKASKTLTKRVQQMIWRIDSLIAQLEMDQRPGKLG

Parental  PANGM-PTGENVISVAELINAMKQVKHIPESKLTSLAAALDENKDGKVNIDDLVKVMELVDKEDVHISTS
          .A......GE.VIS..ELI.AMKQ.K.IPE.KL.SLA..LD..K.GKVNID.L.KV.ELVDK.DVH.STS
Retrocopy QAESSGGVGEKVISITELISAMKQIKNIPENKLISLASTLDKSKNGKVNIDKLIKVIELVDK-DVHVSTS

Parental  QVAEIVATLEKEEK-VEEKEGREGGRRGEA
          QVAE.VA.LEKEE..VEEK....G....EA
Retrocopy QVAEMVAMLEKEER<VEEKKKAKGKAEEEA

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	21.24 RPM
SRP007412_cerebellum	0.00 RPM	16.86 RPM
SRP007412_heart	0.00 RPM	10.13 RPM
SRP007412_kidney	0.00 RPM	22.78 RPM
SRP007412_liver	0.00 RPM	9.39 RPM
SRP007412_testis	0.00 RPM	13.99 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_1158 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1158 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001859	1 retrocopy	retro_cjac_1529,
Homo sapiens	ENSG00000168924	1 retrocopy	retro_hsap_2019,
Gorilla gorilla	ENSGGOG00000002923	2 retrocopies	retro_ggor_1158 , retro_ggor_1159,
Nomascus leucogenys	ENSNLEG00000000067	2 retrocopies	retro_nleu_1752, retro_nleu_2731,
Otolemur garnettii	ENSOGAG00000014883	1 retrocopy	retro_ogar_20,
Pongo abelii	ENSPPYG00000014533	1 retrocopy	retro_pabe_1655,
Ictidomys tridecemlineatus	ENSSTOG00000014167	1 retrocopy	retro_itri_160,