RetrogeneDB ID: retro_opri_789

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_3094:34320..34898(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBP1
• Ensembl ID: ENSOPRG00000004680
• Aliases: None
• Description: poly(rC) binding protein 1 [Source:HGNC Symbol;Acc:8647]

Sequence

>retro_opri_789
ATGGACACCGGTGTGATTGAAGGTGGATTAAATGTCACTCTCACTATTCGGCTACTTATGCATGGCAAGGAAGTTGGCAG
TATCATTGGAAAGAAAGGAGAATCTGTTAAGAAGATGCGCGAGGAGAGCGGTGCACGGATCAACATCTCAGAGGGGAATT
GTCCTGAGAGAATTATCACTTTGGCTGGACCCACTAATGCCATCTTCAAAGCCTTTGCTATGATCATTGACAAACCGGAA
GAGGACATCAGCAGCTCTATGACCAACAGCACAGCTGCCAGCCCACCTCCAGTTACCCTGAGGCTTGTGGTTCCCGCGAG
TCAGAGTGGCTCTCTCATTGGAAAGGGTGGTTGCAAGATCAAGGAAATATGAGAGAGTACAGGGGCTCAGGTGCAGGTGG
CAGGGGACATGCTCCCCAACTCAACTGAGCGCGCCATCACTATTGCTGGCATTCCTCAGTCGATCATTGAGTGTGTTAAA
CAGATCTGCGTGGTCATGTTGGAGTCCCCCCCGAAGGGCGTGACCATCCCATACCGGCCCAAGCTGTCCAGTCTCCGGTC
ATCTTTGCAGGTGGTCAG

Alignment

ORF - retro_opri_789 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.95 %
• Parental protein coverage: 53.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFK
          MDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFK
Retrocopy MDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFK

Parental  AFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
          AFAMIIDK.EEDISSSMTNSTAAS.PPVTLRLVVPASQ.GSLIGKGGCKIKEI.ESTGAQVQVAGDMLPN
Retrocopy AFAMIIDKPEEDISSSMTNSTAASPPPVTLRLVVPASQSGSLIGKGGCKIKEI*ESTGAQVQVAGDMLPN

Parental  STERAITIAGIPQSIIECVKQICVVMLETLSQSPPKGVTIPYRPKPSS-SPVIFAGGQ
          STERAITIAGIPQSIIECVKQICVVMLE....SPPKGVTIPYRPK.SS.SPVIFAGGQ
Retrocopy STERAITIAGIPQSIIECVKQICVVMLE----SPPKGVTIPYRPKLSS<SPVIFAGGQ

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_789 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 7 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000967	2 retrocopies	retro_cpor_193, retro_cpor_97,
Equus caballus	ENSECAG00000022389	1 retrocopy	retro_ecab_67,
Homo sapiens	ENSG00000197111	2 retrocopies	retro_hsap_4077, retro_hsap_83,
Microcebus murinus	ENSMICG00000011651	2 retrocopies	retro_mmur_1226, retro_mmur_1228,
Macaca mulatta	ENSMMUG00000006608	2 retrocopies	retro_mmul_1263, retro_mmul_1994,
Oryctolagus cuniculus	ENSOCUG00000022490	3 retrocopies	retro_ocun_10, retro_ocun_1622, retro_ocun_898,
Ochotona princeps	ENSOPRG00000004680	5 retrocopies	retro_opri_1126, retro_opri_284, retro_opri_313, retro_opri_742, retro_opri_789 ,