RetrogeneDB ID: retro_ogar_1096

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873535.1:19120954..19121878(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAIP1
• Ensembl ID: ENSOGAG00000001887
• Aliases: None
• Description: poly(A) binding protein interacting protein 1 [Source:HGNC Symbol;Acc:16945]

Sequence

>retro_ogar_1096
CCTGGCAGTTTTGAAACTGAAATTGAACAGTTTGCAGAGACCCTGAATGGTTGGGTTACAACAGATGATGCTTTGCAAGA
ACTGGTGGAACTCATCTATCAACAGGCTACATCTGTCCCAAATTTCTCTTATATGGGAGCTCGCCTGTGTAATTACCTGT
CCCATCATCTGACAATTAGCCCACAGAGTGGCGACTTCCGCCAATTACTACTTCAAAGATGTCAGACTGAATATGAAGTT
AAAGATCAAGCTGCAAAAGGGGGTGAAGTTATTCGAAAATGATTTCATGCATTTGTACTCTTTCTGGGAGAACTTTATCT
TAACCTGGAGATCAAGGGAACAAATGGACAGGTTACAAGAGCAGATATTCTTCAGGTTGGTCTCTGAGAATTGCTGAATG
CCCTCTTTTCTAATCCCATGGATGACAACTTAATTTGCGCAGTAAAATTACTGACGCTGACAGGGTCAGTTTTGGAAGAT
GCATGGAAGGAAAAAGGAAAGACTGACATGGAGGAAATTATTCAGAGAATTGAAAATGTTGTCCTAGATGCAAACTGTAG
CAGAGATGTAAAACAGATGCTCCTGAAACTCATGGAACTCGGGTCTAGTAACTGGGGTAGAGTTCATGCAACTTCAACAT
ACAGAGAAGCGACACCTGAAAATGATCCTAACTACTTTATGAATGAACCAACATTTTATTCATCTGATGGTGTTCCTTTT
ACTGCAGCTGATCCGGATTACCAAGAGAACTATCAAGAGTTACTTGAAAGAGAGGGCTTTTATCCAGATTGTGAAGAAAA
CAGAACAGATCTATGATCAGGGGCTGGTGATCCATACTTGGATGATATTGATGATGAGATGGACCTAGAGATAGAAGAAG
CTTATGAGAAGTTTTGTTTGGAATCAGAGCGTAAGTGAAAACAA

Alignment

ORF - retro_ogar_1096 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.83 %
• Parental protein coverage: 63.96 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGSFETEIEQFAETLNGWVTTDDALQELVELIYQQATSIPNFSYMGARLCNYLSHHLTISPQSGNFRQLL
          PGSFETEIEQFAETLNGWVTTDDALQELVELIYQQATS.PNFSYMGARLCNYLSHHLTISPQSG.FRQLL
Retrocopy PGSFETEIEQFAETLNGWVTTDDALQELVELIYQQATSVPNFSYMGARLCNYLSHHLTISPQSGDFRQLL

Parental  LQRCRTEYEVKDQAAKGDEVTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADILQVGLRELLNALFSNPM
          LQRC.TEYEVKDQAAKG.EV.RK.FHAFVLFLGELYLNLEIKGTNGQVTRADILQVGL.ELLNALFSNPM
Retrocopy LQRCQTEYEVKDQAAKGGEVIRK*FHAFVLFLGELYLNLEIKGTNGQVTRADILQVGL*ELLNALFSNPM

Parental  DDNLICAVKLLKLTGSVLEDAWKEKGKTDMEEIIQRIENVVLDANCSRDVKQMLLKLVELRSSNWGRVHA
          DDNLICAVKLL.LTGSVLEDAWKEKGKTDMEEIIQRIENVVLDANCSRDVKQMLLKL.EL.SSNWGRVHA
Retrocopy DDNLICAVKLLTLTGSVLEDAWKEKGKTDMEEIIQRIENVVLDANCSRDVKQMLLKLMELGSSNWGRVHA

Parental  TSTYREATPENDPNYFMNEPTFYTSDGVPFTAADPDYQEKYQELLEREDFFPDYEENGTDL-SGAGDPYL
          TSTYREATPENDPNYFMNEPTFY.SDGVPFTAADPDYQE.YQELLERE.F.PD.EEN.TDL.SGAGDPYL
Retrocopy TSTYREATPENDPNYFMNEPTFYSSDGVPFTAADPDYQENYQELLEREGFYPDCEENRTDL*SGAGDPYL

Parental  DDIDDEMDPEIEEAYEKFCLESERKRKQ
          DDIDDEMD.EIEEAYEKFCLESERK.KQ
Retrocopy DDIDDEMDLEIEEAYEKFCLESERK*KQ

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_1096 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020376	1 retrocopy	retro_btau_359,
Choloepus hoffmanni	ENSCHOG00000004961	1 retrocopy	retro_chof_762,
Callithrix jacchus	ENSCJAG00000001340	2 retrocopies	retro_cjac_3224, retro_cjac_3337,
Erinaceus europaeus	ENSEEUG00000009651	1 retrocopy	retro_eeur_304,
Homo sapiens	ENSG00000172239	1 retrocopy	retro_hsap_1726,
Otolemur garnettii	ENSOGAG00000001887	2 retrocopies	retro_ogar_1096 , retro_ogar_1241,