RetrogeneDB ID: retro_ogar_1093

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873535.1:14029446..14030394(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000033738
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZC3H15
• Ensembl ID: ENSOGAG00000002182
• Aliases: None
• Description: zinc finger CCCH-type containing 15 [Source:HGNC Symbol;Acc:29528]

Sequence

>retro_ogar_1093
GAGCAGAAAAAGAAGGAGAAGATTATCGAAGACAAAACTTTTGGTTTAAAGAATAAGAAAGGACCAAAGCGATAAAAATT
TATCGTGGCTGTCACACATCAAGTTAAATCTGGTCAACAAAATCCACGTCAGGTAGCACAGAGTGAAGCTGAAAAGAAAT
CAAAGAAAGATGAGAGGAAAGAATTGCAGGAACTAAATGCGCTGTTCAAACCTGTAGTTGCTACTCAAAAAATAAGTAAA
GATGCAGATCCCAAATACCTGGTGTGTGCATTCTTCAAGCAAGGACATGTACTAACGGAGATGAGTGTTAAGTTTTCTCA
TGGCTTGACTCTGGAGAGAAAATATGAAAAGAGAAGTGTTTACATGAATGCAAGAGATGAAGAACTTGAAAAAGATACTA
TGGATAATTGGGATGAGAAAAAGCTGGAAGAAGTAGTGAACAAGAAGCACCGTGAGGCGGAAAAGAAAAACCAAAAACCC
AAATAGTATGCAAGCATCTCCTTGAAGCCATTGAAAACAATAAACGTGGCTGGTTTGGGGTATGCCATGGAGGGGGAGAT
ATTTTGCATGTATCGTCATGCACTTCCTCCTGGATTTGTGTTGAAAAAAGATAAAAAGAAAGAAAAAAAAGAAGATGAAA
TTTCATTAGAAGATTTCATCGAGAGAGAGCGTTCCGCCCTAGGTCCAAACGTTACCAAAATCACTCTAGAATCTTTTCTT
GTACGGAAGAAAGGGAAAAGACAAGAGAAAATGGATAAACTTGAACAAGATATGGAAAGAAGGAAAGTGGACTTCAAAGC
AGGGAAAGCATTAGTGATCAGTGGCCGAGAAGTGTTAGAATTTCGTCCTGAGCTGGTCAATGATGATGATGAGGAAGCGG
ATGACACCTGGTATACCCAGGAAACAGGTGGTGATGAGGTTGATGACTCAGTAAGTGTAAAGCCTATA

Alignment

ORF - retro_ogar_1093 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.59 %
• Parental protein coverage: 74.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EQKKKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPRQVAQSEAEKKLKKDDKKKELQELNELF
          EQKKKEKIIEDKTFGLKNKKG.K..KFI.AVTHQVK.GQQNPRQVAQSEAEKK.KKD..K.ELQELN.LF
Retrocopy EQKKKEKIIEDKTFGLKNKKGPKR*KFIVAVTHQVKSGQQNPRQVAQSEAEKKSKKDERK-ELQELNALF

Parental  KPVVAAQKISKGADPKSVVCAFFKQGQ-CTKGDKC-KFSHDLTLERKCEKRSVYIDARDEELEKDTMDNW
          KPVVA.QKISK.ADPK..VCAFFKQG..CT.GD.C.KFSH.LTLERK.EKRSVY..ARDEELEKDTMDNW
Retrocopy KPVVATQKISKDADPKYLVCAFFKQGH<CTNGDEC>KFSHGLTLERKYEKRSVYMNARDEELEKDTMDNW

Parental  DEKKLEEVVNKKHGEAEKK-KPKTQIVCKHFLEAIENNKYGWFWVCPGGGDI-CMYRHALPPGFVLKKDK
          DEKKLEEVVNKKH.EAEKK.KPKTQIVCKH.LEAIENNK.GWF.VC.GGGDI.CMYRHALPPGFVL....
Retrocopy DEKKLEEVVNKKHREAEKK<KPKTQIVCKHLLEAIENNKRGWFGVCHGGGDI>CMYRHALPPGFVLXXXX

Parental  KKEEKEDEISLEDLIERERSALGPNVTKITLESFLAWKKRKRQEKIDKLEQDMERRKADFKAGKALVISG
          ......DEISLED.IERERSALGPNVTKITLESFL..KK.KRQEK.DKLEQDMERRK.DFKAGKALVISG
Retrocopy XXXXXXDEISLEDFIERERSALGPNVTKITLESFLVRKKGKRQEKMDKLEQDMERRKVDFKAGKALVISG

Parental  REVFEFRPELVNDDDEEADDTRYTQGTGGDELKVDDSVSVNDI
          REV.EFRPELVNDDDEEADDT.YTQ.TGGDE..VDDSVSV..I
Retrocopy REVLEFRPELVNDDDEEADDTWYTQETGGDE--VDDSVSVKPI

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_1093 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 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021762	1 retrocopy	retro_btau_1223,
Choloepus hoffmanni	ENSCHOG00000011958	1 retrocopy	retro_chof_2120,
Callithrix jacchus	ENSCJAG00000005931	2 retrocopies	retro_cjac_2883, retro_cjac_3986,
Cavia porcellus	ENSCPOG00000012965	2 retrocopies	retro_cpor_1294, retro_cpor_919,
Dipodomys ordii	ENSDORG00000011664	1 retrocopy	retro_dord_666,
Loxodonta africana	ENSLAFG00000001563	1 retrocopy	retro_lafr_941,
Monodelphis domestica	ENSMODG00000027565	5 retrocopies	retro_mdom_1230, retro_mdom_1321, retro_mdom_1744, retro_mdom_1942, retro_mdom_871,
Oryctolagus cuniculus	ENSOCUG00000011903	1 retrocopy	retro_ocun_886,
Otolemur garnettii	ENSOGAG00000002182	2 retrocopies	retro_ogar_1093 , retro_ogar_611,
Ochotona princeps	ENSOPRG00000015790	2 retrocopies	retro_opri_169, retro_opri_609,
Pan troglodytes	ENSPTRG00000012717	1 retrocopy	retro_ptro_348,
Rattus norvegicus	ENSRNOG00000005256	4 retrocopies	retro_rnor_2628, retro_rnor_284, retro_rnor_662, retro_rnor_925,
Sorex araneus	ENSSARG00000012071	1 retrocopy	retro_sara_363,