RetrogeneDB ID: retro_opri_1174

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_8752:46309..47155(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABPA
• Ensembl ID: ENSOPRG00000009283
• Aliases: None
• Description: GA binding protein transcription factor, alpha subunit 60kDa [Source:HGNC Symbol;Acc:4071]

Sequence

>retro_opri_1174
CTGGATCCAGAGCGAAGTATATTTGACCAAGGAGTAAAGACAGATGGAACTGTACAGCTTAGTGTACAGGTAATTTCTTA
CCGAGGAATTGAGCCGAAGCTGAACATCCTTGAAATTGTTAAAACTGCAGAAACTGTTGAAGTGGTCATTGATCCCGACG
CCCACCATGCTGAAGCTGAGGCACATCTTCTTGAGGAAGCTCAGGTGATAACCCTGGACGGCACCAAGCATATCACCACC
ATTTCAGATGAAACCTCAGAGCAGGTGACGAGATGGGCTGCCGCGCTGGAAGGTTACAGGAAGGAACAAGAACGCCTCGG
GATACCCTATGATCCTATACAGTGGTCCACAGACCAAGTCCTACATTGGGTGGTTTGGGTCATGAAGGAATTCAGCATGA
CTGACATAGATCTCACCACACTCAACATTTCCAGAAGAGAATTATGTAGTCTCAGCCAAGAAGATTTTTTTCAACGAGTC
CCTCGGGGAGAGATTCTTTGGAGTCATCTGGAGCTTCTTCGAAAATATGTGTTGGCAAGCCAAGAGCAACAGATGAATGA
GATAGTCACCATCGATCAACCTGTGCAAATTATTCCCGCTTCAGTGCAGTCAGCCACACCCACTGCCATTAAAGTCCTGA
ACAGCAGTGCCAAAGCAGCCAAAGTCCAGAGGGCTCCACGGATTTCAGAAGACAGGAGATCACCTGGGAACAGAACAGGA
AAAAATGGACAGATCCAGCTATGGCAGTTTTTACTAGAACTCCTTACTGACAAAGATGCTCGAGACTGTATTTCATGGGT
TGGTGATGAAGGTGAATTTAAACTAAATCAACCTGAGCTGGCAGCT

Alignment

ORF - retro_opri_1174 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.46 %
• Parental protein coverage: 74.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDPERSLFDQGVKTDGTVQLSVQVISYQGIEPKLNILEIVKTAETVEVVIDPDAHHAEAEAHLVEEAQVI
          LDPERS.FDQGVKTDGTVQLSVQVISY.GIEPKLNILEIVKTAETVEVVIDPDAHHAEAEAHL.EEAQVI
Retrocopy LDPERSIFDQGVKTDGTVQLSVQVISYRGIEPKLNILEIVKTAETVEVVIDPDAHHAEAEAHLLEEAQVI

Parental  TLDGTKHITTISDETSEQVTRWAAALEGYRKEQERLGIPYDPIQWSTDQVLHWVVWVMKEFSMTDIDLTT
          TLDGTKHITTISDETSEQVTRWAAALEGYRKEQERLGIPYDPIQWSTDQVLHWVVWVMKEFSMTDIDLTT
Retrocopy TLDGTKHITTISDETSEQVTRWAAALEGYRKEQERLGIPYDPIQWSTDQVLHWVVWVMKEFSMTDIDLTT

Parental  LNISGRELCSLSQEDFFQRVPRGEILWSHLELLRKXXXXXXXXXXXXXXXXXXXVQIIPASVQSATPTAI
          LNIS.RELCSLSQEDFFQRVPRGEILWSHLELLRK...................VQIIPASVQSATPTAI
Retrocopy LNISRRELCSLSQEDFFQRVPRGEILWSHLELLRKYVLASQEQQMNEIVTIDQPVQIIPASVQSATPTAI

Parental  KVLNSSAKAAKVQRAPRISGEDRSSPGNRTGNNGQIQLWQFLLELLTDKDARDCISWVGDEGEFKLNQPE
          KVLNSSAKAAKVQRAPRIS.EDR.SPGNRTG.NGQIQLWQFLLELLTDKDARDCISWVGDEGEFKLNQPE
Retrocopy KVLNSSAKAAKVQRAPRIS-EDRRSPGNRTGKNGQIQLWQFLLELLTDKDARDCISWVGDEGEFKLNQPE

Parental  LVA
          L.A
Retrocopy LAA

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_1174 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013817	1 retrocopy	retro_cjac_2487,
Dasypus novemcinctus	ENSDNOG00000016059	1 retrocopy	retro_dnov_476,
Homo sapiens	ENSG00000154727	1 retrocopy	retro_hsap_3737,
Ochotona princeps	ENSOPRG00000009283	1 retrocopy	retro_opri_1174 ,
Pan troglodytes	ENSPTRG00000013810	1 retrocopy	retro_ptro_2536,
Tursiops truncatus	ENSTTRG00000004785	1 retrocopy	retro_ttru_154,