RetrogeneDB ID: retro_ogar_1241

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873540.1:12090458..12091230(+)
• 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_1241
CCTGAATTTTACCCATCAAGTTATTCTTCGAATTATACAGAATCCTATGAGGACAGTTGTGAGGATTATCCCACTCTATC
AGAATATGTTCAGGATTTTTTGAATCATCTTATAGAACAACCTGGCAGTTGTGAAACTGAAATTGAACAGTTTGCAGAGA
CCCTGAATGGCTGGATTACAACAGATAATGCTTTGCAAGAACTGATGGAACTCATCTATCAACAGGCTACATCTATCCCA
AATTTATCTTATATGGGAGCTCACCTGTGTAATTACCTGTCCCATCATCTGACAATTAGCCCACAGAGTGGCAACTTCTG
CCAATTACTACTTCAAAGATGTCGGACTGAATATGAAGTTAAAAATCAAGCTGCAAAAGGAAATGAAGTTACTTGAAAAC
AATTTCATGCATTTGTACTCTTTCTGGGAGAACTTTATCTTAACTTGGAGATCAAAGGAACAAATGGACAGGTTACAAGA
GCAGATATTCTTCAGGTTGGTCTCTGAGAATTGCTGAATGCTCTCTTTTCTAATCCTATGGATGACAACTTAACTTGTCA
GTTAAGTAAAATTACTGAAGTTGACAGGGTCAGTTTTGGAAGATGCATGGAAGGAAAAAGGAAAGACTGACATGGAGGAA
ATTATTCCGAGAATTGAAAATGTTGTCCTAGATGCAAACTGTAGCAGAGATATAAAACAGATGCTCCTGAAACTCGTAGA
ACTCTGGTCTAGTAACTGGGGTAGAGTTCATGCAACTTCTACAGAGAAGCAA

Alignment

ORF - retro_ogar_1241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.76 %
• Parental protein coverage: 53.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PEFYPSSYSSNYTESYEDGCEDYPTLSEYVQDFLNHLTEQPGSFETEIEQFAETLNGWVTTDDALQELVE
          PEFYPSSYSSNYTESYED.CEDYPTLSEYVQDFLNHL.EQPGS.ETEIEQFAETLNGW.TTD.ALQEL.E
Retrocopy PEFYPSSYSSNYTESYEDSCEDYPTLSEYVQDFLNHLIEQPGSCETEIEQFAETLNGWITTDNALQELME

Parental  LIYQQATSIPNFSYMGARLCNYLSHHLTISPQSGNFRQLLLQRCRTEYEVKDQAAKGDEVTRKRFHAFVL
          LIYQQATSIPN.SYMGA.LCNYLSHHLTISPQSGNF.QLLLQRCRTEYEVK.QAAKG.EVT.K.FHAFVL
Retrocopy LIYQQATSIPNLSYMGAHLCNYLSHHLTISPQSGNFCQLLLQRCRTEYEVKNQAAKGNEVT*KQFHAFVL

Parental  FLGELYLNLEIKGTNGQVTRADILQVGLRELLNALFSNPMDDNLICAV-KLLKL-TGSVLEDAWKEKGKT
          FLGELYLNLEIKGTNGQVTRADILQVGL.ELLNALFSNPMDDNL.C...K.....TGSVLEDAWKEKGKT
Retrocopy FLGELYLNLEIKGTNGQVTRADILQVGL*ELLNALFSNPMDDNLTCQLSKITEV>TGSVLEDAWKEKGKT

Parental  DMEEIIQRIENVVLDANCSRDVKQMLLKLVELRSSNWGRVHATSTYRE
          DMEEII.RIENVVLDANCSRD.KQMLLKLVEL.SSNWGRVHATST...
Retrocopy DMEEIIPRIENVVLDANCSRDIKQMLLKLVELWSSNWGRVHATSTEKQ

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_1241 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 ,