RetrogeneDB ID: retro_ogar_3125

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873721.1:1622414..1623752(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000008968
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000034763
• Aliases: None
• Description: None

Sequence

>retro_ogar_3125
ATGACCGTTCCCTCCCCGGTGGAGCTGGCTTCCTTCAAGTACAGTGACCTGCAGAACTTGGCCAAGAGTCTGGGCCTCTG
GGCTAACCTGAGGGCAGACAAGTTGTTAAAAGCCTTAAAAGCCCACCTTAAACAAGACGCAAGAAAAGAAAATAAGAATC
AGGATGAAAGTCAAACTTCTGCATCCTCTTGTGATGAGACTGAGATACAGATTAACAATCAGGAACACGGTGACAGAGAG
CCAGTTGCCCATGTCACCAAAATGAGGAGAAGACACAAGATAGTCCATGGGAACCCTGACTTCCAGCAGGACCATTCAGA
GATCCAAGTAAGTGATTACACCGAATTGCAAAATCATGAAAAGCAGGAAAACCAACATCTCAGTGCTACTGTAAAAGTTC
CTTCTCCATCAGATGAGAGACAAGGAGTTGAAAACACAGTTTCCTCAGGAAGAAGCGGAATAAATGGCAATGGAGAGTCA
AAGGTACCTTCAGAAAGAAAGAAGTCCCTCTACACAAATGAATTTTGCAAACCTAGAAAAATTAAAAGAACTGGCATCAC
TATCCAAACTTTAAGAAGCTTCATGAGGCTCATTTTAAGGAAATGGAGTCCATCGATCAATATATTGAGAGAAAAAAGAA
ACATTTTGAAGGACACAATTCATTTAATGCGCTGAAGAAGCAGCCTGTCAATAAAAGCAGTACAGTGACTCCAGTTCCTC
CAAGAGGAAGACTTTCTGTGCCTTGCACTCCCATCAGCCAACAGGCCCCCAGGGCCACTTTCACACCCCTACAAATGAGA
GCACCTCTGTTCTGAAGGGGTCAGCCAAGCGCTCTGCCCTCTCCACAAGTAAAATGAATGTCAGGTTTTCAGCTGCCAAG
ATAATGAGCATAAGCGTTCACTGACCAAGACTCCAGCCAGAAAGTCTGCACATGTGACCATACCTGGGAGTACCCCAAAA
GGCGAGACTGTGCTCAGGACACACAACTTAAAGACCAGCAAGGAAAATTCTGCTGCTGCTGCTATTACCCCATTCAAGTT
GACAACTGAGGCAATGAAGACTCCAGTCTCTAATAAGAAACCAGTATTTGATCTTAAAGCAAGTTTGTCTTGTCCCCTCA
ACTATGAGCCACACAAAGGAAAACTGAAACCATGGGGACAATCTAAAGAAAACAATTCTCTGAATGTACATGGAAACAGA
GTTAACTTCCACAAGAAAACTTACAAACAACCTCGTCTCCACACTAGGGAGGAGCAACGGAAGAAACATGAGCAACAACG
AAAGGAGAAGAAAGCACAGGTTTTGGGAGCACGAAGAGGACTCGTTATGGCTAAAAGT

Alignment

ORF - retro_ogar_3125 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTVPSPEELDSFKYSDLQNLAKSLGLRANLRADKLLKALKAHLKQEARKENDNQDESQTSASSCDETEIQ
          MTVPSP.EL.SFKYSDLQNLAKSLGL.ANLRADKLLKALKAHLKQ.ARKEN.NQDESQTSASSCDETEIQ
Retrocopy MTVPSPVELASFKYSDLQNLAKSLGLWANLRADKLLKALKAHLKQDARKENKNQDESQTSASSCDETEIQ

Parental  INNQEHGDREPVAHVTKTRRRHKIVHGNPDFQNWQDHSEIQVSDYTELQNHEKQENQHLSATVKVPSPSD
          INNQEHGDREPVAHVTK.RRRHKIVHGNPDFQ..QDHSEIQVSDYTELQNHEKQENQHLSATVKVPSPSD
Retrocopy INNQEHGDREPVAHVTKMRRRHKIVHGNPDFQ--QDHSEIQVSDYTELQNHEKQENQHLSATVKVPSPSD

Parental  ESQGAENTVSS----ILGNGDSKVPSERKKSLYTNEFCKPRKIKRTGITT-PNFKKLHEAHFKEMESIDQ
          E.QG.ENTVSS....I.GNG.SKVPSERKKSLYTNEFCKPRKIKRTGIT..PNFKKLHEAHFKEMESIDQ
Retrocopy ERQGVENTVSSGRSGINGNGESKVPSERKKSLYTNEFCKPRKIKRTGITI<PNFKKLHEAHFKEMESIDQ

Parental  YIERKKKHFEGHNSFNELKKQPVNKSSTVTPVPPRGRLSVPCTPISQQRS-QGRFHTPTNESTSVLKGSA
          YIERKKKHFEGHNSFN.LKKQPVNKSSTVTPVPPRGRLSVPCTPISQQ...QG.FHTPTNESTSVLKGSA
Retrocopy YIERKKKHFEGHNSFNALKKQPVNKSSTVTPVPPRGRLSVPCTPISQQAP<QGHFHTPTNESTSVLKGSA

Parental  KHSALSTSKMNVRFSAATK-DNEHKRSLTKTPARKSAHVTIPGSTPKGKTVLRTHNLKTSKRNSAAAVIT
          K.SALSTSKMNVRFS.A.K.DNEHKRSLTKTPARKSAHVTIPGSTPKG.TVLRTHNLKTSK.NSAAA.IT
Retrocopy KRSALSTSKMNVRFS-AAK<DNEHKRSLTKTPARKSAHVTIPGSTPKGETVLRTHNLKTSKENSAAAAIT

Parental  PFKLTTEAMKTPVSNKKPVFDLKASLSRPLNYEPHKGKLKPWGQSKENNSLNEHGNRVNFHKKTYKQPRL
          PFKLTTEAMKTPVSNKKPVFDLKASLS.PLNYEPHKGKLKPWGQSKENNSLN.HGNRVNFHKKTYKQPRL
Retrocopy PFKLTTEAMKTPVSNKKPVFDLKASLSCPLNYEPHKGKLKPWGQSKENNSLNVHGNRVNFHKKTYKQPRL

Parental  HTREEQRKKHEQQRKEKKAQVLGARRGLIMAKN
          HTREEQRKKHEQQRKEKKAQVLGARRGL.MAK.
Retrocopy HTREEQRKKHEQQRKEKKAQVLGARRGLVMAKS

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_3125 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
Bos taurus	ENSBTAG00000010774	1 retrocopy	retro_btau_1714,
Canis familiaris	ENSCAFG00000009538	3 retrocopies	retro_cfam_1685, retro_cfam_2137, retro_cfam_578,
Cavia porcellus	ENSCPOG00000012875	1 retrocopy	retro_cpor_993,
Cavia porcellus	ENSCPOG00000020956	1 retrocopy	retro_cpor_258,
Myotis lucifugus	ENSMLUG00000009782	1 retrocopy	retro_mluc_389,
Mustela putorius furo	ENSMPUG00000008844	1 retrocopy	retro_mputfur_1626,
Otolemur garnettii	ENSOGAG00000034763	1 retrocopy	retro_ogar_3125 ,
Tupaia belangeri	ENSTBEG00000014283	1 retrocopy	retro_tbel_4088,