RetrogeneDB ID: retro_ggor_1584

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 21:33344995..33346291(-)
• Located in intron of: ENSGGOG00000002047

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMMT
• Ensembl ID: ENSGGOG00000005264
• Aliases: None
• Description: None

Sequence

>retro_ggor_1584
GCCTCATATAAACTTCACAGCACGATAGCTGATCTGGATAATGTGGTCAAAAAGGTCCAAGCAGCTCAATTTGAGGCTAA
GGTTGTATCTCAGTATCATGAGCTGGTGGGCCAAGCTCGGGATGACTTTAAACGACAGCTGGACAGTATTACTCCAGAAG
TCCTTCCTGGGTGGAAAGGAATGAGTGTTTCAGACCCAGCTGACAAGCTCTCTACTGATGATCTGAACTCCCTGATTGCC
CGTGCACATCGTCACATCGATCAGCTGAACAGAGAGCTAGCAGAACAGAAAGCCACAGAAAAGCAGCACATCACATTAGC
CTTGGAGAAACAAACGCTGGAAGAAAAGCGGGCATTTGACTCTGTAGTAGCAAAAGCATTAGAACATCATGGAAGTAAAA
TGCAGGCTGAATAGGACAGAAAGATAGAGGAAGTCAGAGATGCCATGGAGAATGAAATGAGAACCTAGCTTCACTGACAG
GCAGCTGCCCACACTGATCACTTGTGAGATGTCCTTAGGGTTCAAGAACAGGAATTGAAGTATGAATTTGAGCAGAACCT
GTCTGAGAAACTCTCGGAACAAGAATTACAGTTTCGTCATCTCAGTCAAGAGCAAGTTCACAACTTTACTCTGGATATAA
ACACTGCCTATGCCAGACTCAGAGGAATCGAACACGCTGTTCAGAGTCATGCAGTTGCTGAAGAGGAAGCCAGAAAAGCC
TACCAACTCTGGCTTTCAGTGGAGGCATTAAAGTACAGCATGAAGACCTCATCTGCAGAAATGCCTACTGTCCCGCTGGG
TAGTGCAGTTGAGGCCATCAAAGCCAACTGTTCTGATAATGAATTTACCAAAGCTTTAGCCACAGCTATCCCTCCAGAGT
CCCTGACCCATGGGGTGTACAGTGAAGAGACCCTTAGAGCCCGCTTTTTTGCTGTTCAAAAACTGGCCCGAAGGGTAGCA
ATGATTGATTAAACCAGAAATAGCTTGTACCAGTACTTCTTCTCCTACCTGCAGTCCCTGCTTCTATTCCCGCCTCAGCA
ACTGAAGCCGCCCCCAGAGCTCTGATCTGAAGATACAAACACGTTTAAATTACTGTCATATGCCTCCTATTGCATTGAGC
ATGGTGATCTGGAGCTAGCAGCAAAGTTTGTCAATCAGCTGAAGGGGGAATCCAGACGAATGGCACAAGACTGGCTGAAG
GAAGCCCGAATAACCCTAGAAACGAAACAGATAGTGGAAATCCTGACAGCATATGCCAGCGCCGTAGGCACAAGAACCAC
TCAAGTACAGCCAGAG

Alignment

ORF - retro_ggor_1584 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.22 %
• Parental protein coverage: 57.97 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEGKLHNMIVDLDNVVKKVQAAQSEAKVVSQYHELVVQARDDFKRELDSITPEVLPGWKGMSVSDLADKL
          A..KLH..I.DLDNVVKKVQAAQ.EAKVVSQYHELV.QARDDFKR.LDSITPEVLPGWKGMSVSD.ADKL
Retrocopy ASYKLHSTIADLDNVVKKVQAAQFEAKVVSQYHELVGQARDDFKRQLDSITPEVLPGWKGMSVSDPADKL

Parental  STDDLNSLIAHAHRRIDQLNRELAEQKATEKQHITLALEKQKLEEKRAFDSAVAKALEHHRSEIQAEQDR
          STDDLNSLIA.AHR.IDQLNRELAEQKATEKQHITLALEKQ.LEEKRAFDS.VAKALEHH.S..QAE.DR
Retrocopy STDDLNSLIARAHRHIDQLNRELAEQKATEKQHITLALEKQTLEEKRAFDSVVAKALEHHGSKMQAE*DR

Parental  KIEEVRDAMENEMRTQLRRQAAAHTDHLRDVLRVQEQELKSEFEQQNMGRRYSQFEKYYPRLPKQHVSGL
          KIEEVRDAMENEMRT.L..QAAAHTDHL.DVLRVQEQELK.EFEQ.N.....S..E.....L....V...
Retrocopy KIEEVRDAMENEMRT*LH*QAAAHTDHL*DVLRVQEQELKYEFEQ-NLSEKLSEQELQFRHLSQEQVHNF

Parental  TGDMQAAHVRLRGIEQAVQSHAVAEEEARKAHQLWLSVEALKYSMKTSSAEMPTVPLGSAVEAIKANCSD
          T.D...A..RLRGIE.AVQSHAVAEEEARKA.QLWLSVEALKYSMKTSSAEMPTVPLGSAVEAIKANCSD
Retrocopy TLDINTAYARLRGIEHAVQSHAVAEEEARKAYQLWLSVEALKYSMKTSSAEMPTVPLGSAVEAIKANCSD

Parental  NEFTQALTAAIPPESLTRGVYSEETLRARFYAVQKLARRVAMIDETRNSLYQYFLSYLQSLLLFPPQQLK
          NEFT.AL..AIPPESLT.GVYSEETLRARF.AVQKLARRVAMID.TRNSLYQYF.SYLQSLLLFPPQQLK
Retrocopy NEFTKALATAIPPESLTHGVYSEETLRARFFAVQKLARRVAMID*TRNSLYQYFFSYLQSLLLFPPQQLK

Parental  PPPELCPEDINTFKLLSYASYCIEHGDLELAAKFVNQLKGESRRVAQDWLKEARMTLETKQIVEILTAYA
          PPPEL..ED.NTFKLLSYASYCIEHGDLELAAKFVNQLKGESRR.AQDWLKEAR.TLETKQIVEILTAYA
Retrocopy PPPEL*SEDTNTFKLLSYASYCIEHGDLELAAKFVNQLKGESRRMAQDWLKEARITLETKQIVEILTAYA

Parental  SAVGIGTTQVQPE
          SAVG..TTQVQPE
Retrocopy SAVGTRTTQVQPE

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	0.82 RPM	41.48 RPM
SRP007412_cerebellum	0.67 RPM	26.83 RPM
SRP007412_heart	0.56 RPM	48.44 RPM
SRP007412_kidney	0.90 RPM	46.08 RPM
SRP007412_liver	0.47 RPM	21.16 RPM
SRP007412_testis	2.80 RPM	85.47 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_1584 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1584 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2535
Pan troglodytes	retro_ptro_1478

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000132305	1 retrocopy	retro_hsap_2535,
Gorilla gorilla	ENSGGOG00000005264	1 retrocopy	retro_ggor_1584 ,
Pan troglodytes	ENSPTRG00000012150	1 retrocopy	retro_ptro_1478,