RetrogeneDB ID: retro_ogar_1041

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873534.1:29015061..29016540(+)
• Located in intron of: None

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_1041
GCTATTAGAACGAGCCTTGGACCAAAAGGAATGGAAAAAATGATTCAAGATGGGAAAGGTGATGTGACTATCACAAACGA
TGGGGCCACCATTTTGAAACAATTGCAGGTATTGCATCCAGCAGCCTGAATGCTGGTGGAGCTGTCCAAGGCTCAAGATA
AAGAATCAGGAGATGGCACTACATCAGTAGTCATCGTTGCTGGCTCACTCTTAGATTCTTGTACCAAGCTTCTTCAGAAA
GGCATTCATCCTACCGTCATTTCCAGGTCATTCCAGAAGGCTTTGGAAAACGGTATTGAAATCTTGAATGACATGTCTCG
ACCTGTGGAACTAAGTGACAGAGAAACTTTGTTAAGTAGTGCAACCACTTCATTGAACTCCAAGGTTGTCTCTCAGTATT
CAAGTCTACTTTCTCCAATGAGTGTAAATGCAGTGATGAAAGTGATTGACCCAGCCACAGCTACTAGTGTAGATCTTAGA
GATATTAAAATAGTTAAGAAGCTTGGTGGAACAATTGATGACTGTGAATTGGTGGAAGGACTGGTTCTCATCCAAAAGGT
GGCAAATTCTGGCATAACCAGAGTTGAAAAGGCTAAGATTGGGCTTATTCAGTTTTGCTTATCTGCTCCCAAAACAGACA
TGGATAATCAAATAGTGGTTTCTGACTATGCCCAAATGGACCGAGTGCTGAGAGAAGAGAGAGCCTATATCTTAAACTTA
GTGAAGCAAATTAAAAAAAACAAGATGTAATGTCCTTCTCATATAGAAGTCTATTCTAAGAGATGCTCTTAGTGATCTTG
CATTACATTTTTTGAACAAAATGAAGATTATGGTGATTAAGGATATTGAAAGAGAAGACATTGAATTCATTTGTAAGACA
ATTGGAACCAAACCAGTTGCTCATATTGACCAATTCACTGCTGACATGTTGGGCTCTGCTGAGTTAGCTGAGGAAGTCAA
TTTAAATGGTTCTGGCAAACTGCTCAAGATTACAGGCTGTGCCTGTCCTGGGAAAACAGTTACAGTCGTCGTTCGTGGCT
CTAACTACTGGTGATTGAAGAGGGTGACCACTCCATTCATGATGCCCTATGTGTTATTCGCTGTTTAGTGAAGAAAAGAG
CCCTTATTGCAGGAGGTGGTGCTCCAGAAATAGAGTTGGCCCTCCGATTAACTGAATATTCATGAACATTGAGTGGTATG
GAATCCTATTCTGTCTGTGCTTTTGCAGATGCTAAGGAGGTCTTTCCATCTACACTAGCTGAAAATGCTGGTCCGAATCC
CATTTCTACAGTAACAGAACTAAGAAACCGGCATGCCCAAGGAGAAAAAAGTACAGGCATTAATGTCCGAAAGGGTGGCA
TTTCCAACATTTTGGAGGAGCTAGTTGTCCAGCCTCTGTTGGTTTCAGTCAGTGCTTTGACCCTAGCAACTGAAACTGTT
CGGAGCATTCTGAAAATTGATGATGTGGTAAACACACGA

Alignment

ORF - retro_ogar_1041 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.73 %
• Parental protein coverage: 91.47 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AIRTSLGPKGMDKMIQDGKGDVTITNDGATILKQMQVLHPAARMLVELSKAQDIEAGDGTTSVVIIAGSL
          AIRTSLGPKGM.KMIQDGKGDVTITNDGATILKQ.QVLHPAA.MLVELSKAQD.E.GDGTTSVVI.AGSL
Retrocopy AIRTSLGPKGMEKMIQDGKGDVTITNDGATILKQLQVLHPAA*MLVELSKAQDKESGDGTTSVVIVAGSL

Parental  LDSCTKLLQKGIHPTIISESFQKALEK-VEILNDMSRPVELSDRETLLNSATTSLNSKVVSQYSSLLSPM
          LDSCTKLLQKGIHPT.IS.SFQKALE...EILNDMSRPVELSDRETLL.SATTSLNSKVVSQYSSLLSPM
Retrocopy LDSCTKLLQKGIHPTVISRSFQKALENGIEILNDMSRPVELSDRETLLSSATTSLNSKVVSQYSSLLSPM

Parental  SVNAVMKVIDPATATSVDLRDIKIVKKLGGTIDDCELVEGLVLVQKVANSGITRVEKAKXTYLPSLLQKK
          SVNAVMKVIDPATATSVDLRDIKIVKKLGGTIDDCELVEGLVL.QKVANSGITRVEKAK.......L...
Retrocopy SVNAVMKVIDPATATSVDLRDIKIVKKLGGTIDDCELVEGLVLIQKVANSGITRVEKAKIGLIQFCLSAP

Parental  KKDIMDNQIVVSDYAQMDRVLREERAYILNLVKQIKKTG-CNVLLIQKSILRDALSDLALHFLNKMKIMV
          K.D.MDNQIVVSDYAQMDRVLREERAYILNLVKQI.....CNVLLI.KSILRDALSDLALHFLNKMKIMV
Retrocopy KTD-MDNQIVVSDYAQMDRVLREERAYILNLVKQIXXXK>CNVLLI*KSILRDALSDLALHFLNKMKIMV

Parental  IKDIEREDIEFICKTIGTKPVAHIDQFTPDMLGSAELAEEVNLNGSGKLLKITGCASPGKTVTIVVRGSN
          IKDIEREDIEFICKTIGTKPVAHIDQFT.DMLGSAELAEEVNLNGSGKLLKITGCA.PGKTVT.VVRGSN
Retrocopy IKDIEREDIEFICKTIGTKPVAHIDQFTADMLGSAELAEEVNLNGSGKLLKITGCACPGKTVTVVVRGSN

Parental  K-LVIEEAERSIHDALCVIRCLVKKRALIAGGGAPEIELALRLTEYSRTLSGMESYCVRAFADAMEVIPS
          ..LVIEE...SIHDALCVIRCLVKKRALIAGGGAPEIELALRLTEYS.TLSGMESY.V.AFADA.EV.PS
Retrocopy Y<LVIEEGDHSIHDALCVIRCLVKKRALIAGGGAPEIELALRLTEYS*TLSGMESYSVCAFADAKEVFPS

Parental  TLAENAGLNPISTVTELRNRHAQGEKTTGINVRKGGISNILEELVVQPLLVSVSALTLATETVRSILKID
          TLAENAG.NPISTVTELRNRHAQGEK.TGINVRKGGISNILEELVVQPLLVSVSALTLATETVRSILKID
Retrocopy TLAENAGPNPISTVTELRNRHAQGEKSTGINVRKGGISNILEELVVQPLLVSVSALTLATETVRSILKID

Parental  DVVNTR
          DVVNTR
Retrocopy DVVNTR

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_1041 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,