RetrogeneDB ID: retro_opri_469

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_12936:8567..9562(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAIP1
• Ensembl ID: ENSOPRG00000000386
• Aliases: None
• Description: poly(A) binding protein interacting protein 1 [Source:HGNC Symbol;Acc:16945]

Sequence

>retro_opri_469
GAATCCTATGAAGATGGGTGTGAGGAATAGCCCACTCTATCAGAGTACGTTCAGGACTTTTGGAATCATCTCACAGAACA
GCCTGGCAATTTTGAAACTGAAATTGAACAGTTTGCAGAGACCCTGAACGGTTGGGTTACAACAGATGATGCTTTGCAAG
AACTTGTCGAACTCATCTATCAACAGGCTACGTCTATCCCAAACTTCTCTTACATGGGAGCTCGCCTGTGTAATTACTTG
TCCCATCATCTGACAATTAGCCCACAGAGTGGCAACTTTCGTCAATTGCTACTTCAAAGGTGTCGGACTGAGTATGAAGT
GAAAGATCAAGCTGCGAAAGGGGATGAAGTGACTCGGAAACGGTTCATGCGTTTGTCCTCTTCCTCGGAGAGCGCTTCCT
TAACCTGGAGACCAAGGGAACAAATGGACAGGCTATGAGAGCAGATATTCTTCCAGTTGGTCTTCGAGAGTTGCTGAATG
CGCTTTTTTCTAATCCTATGGATGACAACTTAATCTGTGCAGTGAAATTACTGAAGTTGACAGGATCCGTTTTGGAAGAT
GCCTGGAAGGAAAAAGCCAAGACTGATATGGAAGAAATTATTCAGAGAATTGAAAATGTTGTCCTTGATGCTAACTGCAG
CAGAGACGTAAAGCTCCCGAAGCTGGTGGAGCTCTGGTCAAGTAGCTGGGGTAGAGTCCATGCAATTTCAGCCTACAGAG
AAGCAACACCTGAGAATGATCCTAACTACTTCATGAACGAACCAACATTTTATACATCCGATGGTGTTCCTTTCACCGCA
GCTGATCCAGATTACCAAGAGAAATATCAAGAATTACTTGAACGAGAAGATTTTTTCCCGGATTATGAAGAAAATGGAAC
AGATTTATCCGGGGCTGGTGATCCATACTTGGGTGATATTGATGATGAGATGGACCCAGAGATAGAAGAAGCTTATGAAA
AGTTTCGTTTGAAATCAGAGCGTAAGCGAAAGCAA

Alignment

ORF - retro_opri_469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.33 %
• Parental protein coverage: 69.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESYEDGCEEYPTLSEYVQDFLNHLTEQPGSFETEIEQFAETLNGWVTTDDALQELVELIYQQATSIPNFS
          ESYEDGCEE.PTLSEYVQDF.NHLTEQPG.FETEIEQFAETLNGWVTTDDALQELVELIYQQATSIPNFS
Retrocopy ESYEDGCEE*PTLSEYVQDFWNHLTEQPGNFETEIEQFAETLNGWVTTDDALQELVELIYQQATSIPNFS

Parental  YMGARLCNYLSHHLTISPQSGNFRQLLLQRCRTEYEVKDQAAKGDEVTRKRF-HAFVLFLGELFLNLEIK
          YMGARLCNYLSHHLTISPQSGNFRQLLLQRCRTEYEVKDQAAKGDEVTRKRF.HAFVLFLGE.FLNLE.K
Retrocopy YMGARLCNYLSHHLTISPQSGNFRQLLLQRCRTEYEVKDQAAKGDEVTRKRF<HAFVLFLGERFLNLETK

Parental  GTNGQVMRADILQVGLRELLNALFSNPMDDNLICAVKLLKLTGSVLEDAWKEKAKTDMEEIIQRIENVVL
          GTNGQ.MRADIL.VGLRELLNALFSNPMDDNLICAVKLLKLTGSVLEDAWKEKAKTDMEEIIQRIENVVL
Retrocopy GTNGQAMRADILPVGLRELLNALFSNPMDDNLICAVKLLKLTGSVLEDAWKEKAKTDMEEIIQRIENVVL

Parental  DANCSRDVKQMLLKLVELRSSNWGRVHATSTYREATPENDPNYFMNEPTFYTSDGVPFTAADPDYQEKYQ
          DANCSRDVK..L.KLVEL.SS.WGRVHA.S.YREATPENDPNYFMNEPTFYTSDGVPFTAADPDYQEKYQ
Retrocopy DANCSRDVK--LPKLVELWSSSWGRVHAISAYREATPENDPNYFMNEPTFYTSDGVPFTAADPDYQEKYQ

Parental  ELLEREDFFPDYEENGTDLSGAGDPYLDDIDDEMDPEI-EAYEKFCLESERKRKQ
          ELLEREDFFPDYEENGTDLSGAGDPYL.DIDDEMDPEI.EAYEKF.L.SERKRKQ
Retrocopy ELLEREDFFPDYEENGTDLSGAGDPYLGDIDDEMDPEIEEAYEKFRLKSERKRKQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_469 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020376	1 retrocopy	retro_btau_359,
Cavia porcellus	ENSCPOG00000002525	2 retrocopies	retro_cpor_133, retro_cpor_197,
Erinaceus europaeus	ENSEEUG00000009651	1 retrocopy	retro_eeur_304,
Ochotona princeps	ENSOPRG00000000386	2 retrocopies	retro_opri_185, retro_opri_469 ,
Ictidomys tridecemlineatus	ENSSTOG00000011203	1 retrocopy	retro_itri_234,