RetrogeneDB ID: retro_ogar_1070

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873535.1:13562938..13563813(+)
• Located in intron of: ENSOGAG00000016062

Retrocopy information

• Ensembl ID: ENSOGAG00000034110
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DAZL
• Ensembl ID: ENSOGAG00000006983
• Aliases: None
• Description: deleted in azoospermia-like [Source:HGNC Symbol;Acc:2685]

Sequence

>retro_ogar_1070
TCTGCTGCAAATCCTGAGACTCCAAACTCAACTATCTCCAGGGAGGCTACACCCAGTCCATCTACAACCAGCCACAGCTA
TGTTTTACCAGAAGGCAAAATCATGCCAAATACCGTTTTTGTTGGTGGAACTGATGTCAGGATGGATGAAACCGAAATGA
GAAGTTTCTTTGCTAGATATGGTTCAGTAAAAGAAATGAAGATAATCACGGACCGAACTGGTGTGTCCAAAGGCTATGGA
TTTGTTTCATTTTATAATGATGTGGATGTGCAGAAGATAGTAGAAACACAGATAAAATTTCTGTAAAAAGCTGAAACTGG
GCTCTGCAATCAGGAAACAAAATTTATGTGCTTGTCATGTGCAGCCACGTCCTTTGGTTTTTAATCCTCCTCCTCCACCC
CAGTTTCAGAGTGTCTGGAGTAATCCAAACACTGAAACTTTATATGTAGCCTCCAACCATGATGAATCCTGTAACTCAAT
ATGTTCAGGCATATCCTCCTTATCCAAGTTCACCAGTTCAGGTCATCACAGGATATCAGCTGCCTGTATCTAACTATCAG
ATGCCACCACAGTGGCCTGCTGGAGAACAACGGATTTATGTTATACCTCCGGCTTATACAGCTGTTAATTACCACTGTGA
TGAAGTTGATCCAGGAGCTGAAGTTTTGCCAAATGAATGCTCAGTTCATGAAGCTACTCCATCTTCTGGAAATGGCCCAC
AAAAGAAATCTGTGGACCGAAGCATTCAGACAGTGGTATCTTGTCTGTTTAACCCAGAGAATAGACTGAGAAACTCCCTT
GTTACCCAAGATGACTATTTCAAGGATAAAAGAGTGCATCACTTTAGAAGAAGCCAGGCAATGCTTAACTCTGTT

Alignment

ORF - retro_ogar_1070 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.89 %
• Parental protein coverage: 99.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SAANPETPNSTISREASTQSSSSTTSQGYVLPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKI
          SAANPETPNSTISREA....S.STTS..YVLPEGKIMPNTVFVGG.DVRMDETE.RSFFARYGSVKE.KI
Retrocopy SAANPETPNSTISREATP--SPSTTSHSYVLPEGKIMPNTVFVGGTDVRMDETEMRSFFARYGSVKEMKI

Parental  ITDRTGVSKGYGFVSFYNDVDVQKIVESQI-NFHGKKLKLGPAIRKQNLCAYHVQPRPLVFNPPPPPQFQ
          ITDRTGVSKGYGFVSFYNDVDVQKIVE.QI.NF..KKLKLG.AIRKQNLCA.HVQPRPLVFNPPPPPQFQ
Retrocopy ITDRTGVSKGYGFVSFYNDVDVQKIVETQI>NFC-KKLKLGSAIRKQNLCACHVQPRPLVFNPPPPPQFQ

Parental  SVWSNPNTET-YMQPPTMMNPITQYVQAYPPYPSSPVQVITGYQLPVYNYQMPPQWPAGEQRSYVIPPAY
          SVWSNPNTET.YM.PPTMMNP.TQYVQAYPPYPSSPVQVITGYQLPV.NYQMPPQWPAGEQR.YVIPPAY
Retrocopy SVWSNPNTET>YM*PPTMMNPVTQYVQAYPPYPSSPVQVITGYQLPVSNYQMPPQWPAGEQRIYVIPPAY

Parental  TAVNYHCNEVDPGAEVLPNECSVHEATPSSGNGPQKKSVDRSIQTVVSCLFNPENRLRNSLVTQDDYFKD
          TAVNYHC.EVDPGAEVLPNECSVHEATPSSGNGPQKKSVDRSIQTVVSCLFNPENRLRNSLVTQDDYFKD
Retrocopy TAVNYHCDEVDPGAEVLPNECSVHEATPSSGNGPQKKSVDRSIQTVVSCLFNPENRLRNSLVTQDDYFKD

Parental  KRVHHFRRSRAMLKSV
          KRVHHFRRS.AML.SV
Retrocopy KRVHHFRRSQAMLNSV

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_1070 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007628	1 retrocopy	retro_cpor_637,
Otolemur garnettii	ENSOGAG00000006983	1 retrocopy	retro_ogar_1070 ,
Pteropus vampyrus	ENSPVAG00000007836	2 retrocopies	retro_pvam_1185, retro_pvam_674,