RetrogeneDB ID: retro_opri_1149

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_80356:2..728(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAE1
• Ensembl ID: ENSOPRG00000000228
• Aliases: None
• Description: RAE1 RNA export 1 homolog (S. pombe) [Source:HGNC Symbol;Acc:9828]

Sequence

>retro_opri_1149
GATGCTCCTGTTAAAACCATACACTGGATCATAGCCGCCAACTACAGCTGTGAGATGACCTGGAACTGGGATAAGACTCT
GAAGTTCTGGGACATCAGGTCGTCAAACCCCATGATATTTTGCAACTCCCTGAGAGGTGTTACTGTGCTGACGTGATATA
CCCGATTGCCGTGGTGGCGACAGCAGAGAGGGGCCTGATTGTCTATTAGTTGGAGAACCAGCCGTACGGGTTCAGGAGGA
CAGAATCCACGCTGAAACATCAGCATCCGTGTGTGGCTATTTTTAAAGACAAACAGAACAAACCAACTGGATTTGCTCTC
GGAAGTATTGAGGGGAGAGTTGCTATTCACTACATCAATCCTCCAAATCCTGCCAAAGATAACTTCACCTTTAAATGCCA
TCGATCCAATGGGACCAACACTTCTGTCCCTCAAGACATCTATGCGGTCAACGGCATCGCCTTCCACCCCGTTCACGGCA
CCCTGACCACCATGGGATCTGATGGCCGCCTCAGCTTCTGGGACAAAGATGCCAGAACAAAACTCAAAACTTCAGAGCAG
TTAGATCAGCCGATAGCAGCCTGCTGCTTCAACCACAACGGGAACATATTTGCACATGCTTCCAGCTACGACTAGTCCAA
GGGACATGAGTTTTACAATCCTCAAAAGAAAAAAATACATTTTCCTGCGGAATGCAGCTGAAGAACTAAAGCCCAGGAAT
AAGAAG

Alignment

ORF - retro_opri_1149 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.16 %
• Parental protein coverage: 65.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMM-VLQLPERCYCADVIYPMAVVATAERGLIVY
          DAPVKTIHWI.A.NYSC.MT..WDKTLKFWD.RSSNPM...LQLPERCYCADVIYP.AVVATAERGLIVY
Retrocopy DAPVKTIHWIIAANYSCEMTWNWDKTLKFWDIRSSNPMI<ILQLPERCYCADVIYPIAVVATAERGLIVY

Parental  QLENQPSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGT
          .LENQP..FRR.ES.LKHQH.CVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGT
Retrocopy *LENQPYGFRRTESTLKHQHPCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGT

Parental  NTSAPQDIYAVNGIAFHPVHGTLATVGSDGRFSFWDKDARTKLKTSEQLDQPIAACCFNHNGNIFAYASS
          NTS.PQDIYAVNGIAFHPVHGTL.T.GSDGR.SFWDKDARTKLKTSEQLDQPIAACCFNHNGNIFA.ASS
Retrocopy NTSVPQDIYAVNGIAFHPVHGTLTTMGSDGRLSFWDKDARTKLKTSEQLDQPIAACCFNHNGNIFAHASS

Parental  YDWSKGHEFYNPQK-KNYIFLRNAAEELKPRNKK
          YD.SKGHEFYNPQK.K.YIFLRNAAEELKPRNKK
Retrocopy YD*SKGHEFYNPQK>KKYIFLRNAAEELKPRNKK

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_1149 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
Oryctolagus cuniculus	ENSOCUG00000001585	2 retrocopies	retro_ocun_1819, retro_ocun_646,
Otolemur garnettii	ENSOGAG00000014649	2 retrocopies	retro_ogar_1400, retro_ogar_2829,
Ochotona princeps	ENSOPRG00000000228	1 retrocopy	retro_opri_1149 ,
Sarcophilus harrisii	ENSSHAG00000000550	1 retrocopy	retro_shar_812,
Sarcophilus harrisii	ENSSHAG00000002438	1 retrocopy	retro_shar_811,