RetrogeneDB ID: retro_ogar_1931

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873574.1:10869695..10871264(-)
• Located in intron of: ENSOGAG00000004117

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT4
• Ensembl ID: ENSOGAG00000003974
• Aliases: None
• Description: chaperonin containing TCP1, subunit 4 (delta) [Source:HGNC Symbol;Acc:1617]

Sequence

>retro_ogar_1931
ATGCCTGAGAACGTGGCACCCCGGAGCGGATCGCCCGCCAGTGCTCCCGGTGGCCACGGAAAGGTCGCTTATCAGGACCG
CGACAAGCCAGCCCAAATCCGCTTCAGCAACATTTCTGGAGCCAAAGCTGTTGCTGATGCTATTAGAACGAGCCTTGGAC
CAAAAGGAATGGATAAAATGATTCAAGATGAGAAAGGTGATGTGACTATCACAAACGATGGGGCCAGCATTTTGAAACAA
ATGCAGGTATTGTATCCAGCAGCCAGAATGCTGGTGGAGCTGTCCAAGGCTCAAGATATAGAAGCAGGAGATGGCACTAC
AGTAGTCATCATTGCTGGCTCGCTCTTAGATTCTTGTACCAAGCTTCTTCAGAAAGGGATTCATCCTACCATCATTTCTG
AGTCATTCCAGAAGGCTTTGGAAAAGGGTATTGAAATCTTGAATGACATGTCTCGACCTGTGGAACTAAGTGACAGAGAA
ACTTTGTTAAATAGTGCAACCACTTCGTTGAACTCCAAGGTTGTCTCTCAGTATTCAAGTCTACTTTCTCCAATGAGTGT
AAATGCAGTGATGAAAGTGATTGACCCAACCACAGCTACTAGTGTAGATCTTGGAGATATTAAAATAGTTAAGAAGCTTG
GTGGAACAATTGATGACTGTGAATTGGTGGAAGGACTGGTTCTCGTCCAAAAGGTGGCAAATTCTGGCATAACCAGAGTT
GAAAAGGCTAAGATTGGGCTTATTCAGTTTTGCTTATCTGCTCCCAAAACAGACATGGATAATCAAATAGTGGTTTCTGA
CTATGCCCAGATGGACCGAGTGCTGAGAGAAGAGAGAGCCTGTATCTTAAACTTAGTGAAGCAAATTAAAAAAACAGGAT
GTAATGTCCTTCTCATATAGAAGTCTATTCTAAGAGATGCTCTTAGTGATCTTGCATTACATTTTTTGAACAAAATGAAG
ATTATGGTGATTAAGGATATTGAAAGAGAAGACATTGAATTCATTTGTAAGACAATTGGAACCAAACCAGTTGCTCATAT
TGAGCAAGTCACTGCTGACATGTTGGGCTCTGCTGAGTTAGCTGAGGAAGTCAATTTAAATGGTTCTGGCAAACTGCTCA
AGATTACAGGCTGTGCCAGTCCTGGGAAAACAGTTACAGTCGTCGTTCGTGGCTCTAACAAACTGGTGATTGAAGAGGCT
GAGTGCTCCATTCATGATGCCCTATGTGTTATTCGCTGTTTAGTGAAGAAAAGAGCCCTTATTACAGGAGGTGGTGCTCC
AGAAATAGAGTTGGCCCTCCGATTAACTGAATATTCACGAACATTGAGTGGTATGGAATCCTATTGCATCCGTGCTTTTG
CAGATGCTATGGAGGTCATTCCATCTACACTAGCTGAAAATGCTGGTCTGAATCCCATTTCTACAGTAACAGAACTGAGA
AACCGGCATGCCCAAGGAGAAAAAACTACAGGCATTAATGTCCAAAAGGGTGGCATTTCCAACATTTTGGAGGAGCTAGT
TGTCCAGCCTCTGTTGGTTTCAGTCAGTGCTTTGACCCTAGCAACTGAA

Alignment

ORF - retro_ogar_1931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.33 %
• Parental protein coverage: 97.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPENVAPRSGAPAGAPGGRGKGAYQDRDKPAQIRFSNISAAKAVADAIRTSLGPKGMDKMIQDGKGDVTI
          MPENVAPRSG.PA.APGG.GK.AYQDRDKPAQIRFSNIS.AKAVADAIRTSLGPKGMDKMIQD.KGDVTI
Retrocopy MPENVAPRSGSPASAPGGHGKVAYQDRDKPAQIRFSNISGAKAVADAIRTSLGPKGMDKMIQDEKGDVTI

Parental  TNDGATILKQMQVLHPAARMLVELSKAQDIEAGDGTTSVVIIAGSLLDSCTKLLQKGIHPTIISESFQKA
          TNDGA.ILKQMQVL.PAARMLVELSKAQDIEAGDGTT.VVIIAGSLLDSCTKLLQKGIHPTIISESFQKA
Retrocopy TNDGASILKQMQVLYPAARMLVELSKAQDIEAGDGTT-VVIIAGSLLDSCTKLLQKGIHPTIISESFQKA

Parental  LEK-VEILNDMSRPVELSDRETLLNSATTSLNSKVVSQYSSLLSPMSVNAVMKVIDPATATSVDLRDIKI
          LEK..EILNDMSRPVELSDRETLLNSATTSLNSKVVSQYSSLLSPMSVNAVMKVIDP.TATSVDL.DIKI
Retrocopy LEKGIEILNDMSRPVELSDRETLLNSATTSLNSKVVSQYSSLLSPMSVNAVMKVIDPTTATSVDLGDIKI

Parental  VKKLGGTIDDCELVEGLVLVQKVANSGITRVEKAKXTYLPSLLQKKKKDIMDNQIVVSDYAQMDRVLREE
          VKKLGGTIDDCELVEGLVLVQKVANSGITRVEKAK.......L...K.D.MDNQIVVSDYAQMDRVLREE
Retrocopy VKKLGGTIDDCELVEGLVLVQKVANSGITRVEKAKIGLIQFCLSAPKTD-MDNQIVVSDYAQMDRVLREE

Parental  RAYILNLVKQIKKTGCNVLLIQKSILRDALSDLALHFLNKMKIMVIKDIEREDIEFICKTIGTKPVAHID
          RA.ILNLVKQIKKTGCNVLLI.KSILRDALSDLALHFLNKMKIMVIKDIEREDIEFICKTIGTKPVAHI.
Retrocopy RACILNLVKQIKKTGCNVLLI*KSILRDALSDLALHFLNKMKIMVIKDIEREDIEFICKTIGTKPVAHIE

Parental  QFTPDMLGSAELAEEVNLNGSGKLLKITGCASPGKTVTIVVRGSNKLVIEEAERSIHDALCVIRCLVKKR
          Q.T.DMLGSAELAEEVNLNGSGKLLKITGCASPGKTVT.VVRGSNKLVIEEAE.SIHDALCVIRCLVKKR
Retrocopy QVTADMLGSAELAEEVNLNGSGKLLKITGCASPGKTVTVVVRGSNKLVIEEAECSIHDALCVIRCLVKKR

Parental  ALIAGGGAPEIELALRLTEYSRTLSGMESYCVRAFADAMEVIPSTLAENAGLNPISTVTELRNRHAQGEK
          ALI.GGGAPEIELALRLTEYSRTLSGMESYC.RAFADAMEVIPSTLAENAGLNPISTVTELRNRHAQGEK
Retrocopy ALITGGGAPEIELALRLTEYSRTLSGMESYCIRAFADAMEVIPSTLAENAGLNPISTVTELRNRHAQGEK

Parental  TTGINVRKGGISNILEELVVQPLLVSVSALTLATE
          TTGINV.KGGISNILEELVVQPLLVSVSALTLATE
Retrocopy TTGINVQKGGISNILEELVVQPLLVSVSALTLATE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_1931 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003083	2 retrocopies	retro_cfam_2093, retro_cfam_590,
Callithrix jacchus	ENSCJAG00000008703	1 retrocopy	retro_cjac_724,
Equus caballus	ENSECAG00000016982	1 retrocopy	retro_ecab_148,
Microcebus murinus	ENSMICG00000015263	1 retrocopy	retro_mmur_344,
Macaca mulatta	ENSMMUG00000013973	1 retrocopy	retro_mmul_2500,
Monodelphis domestica	ENSMODG00000002882	1 retrocopy	retro_mdom_1402,
Otolemur garnettii	ENSOGAG00000003974	2 retrocopies	retro_ogar_1041, retro_ogar_1931 ,
Sorex araneus	ENSSARG00000010539	1 retrocopy	retro_sara_7,