RetrogeneDB ID: retro_opri_952

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_4947:51116..51909(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMSS1
• Ensembl ID: ENSOPRG00000002986
• Aliases: None
• Description: cms1 ribosomal small subunit homolog (yeast) [Source:HGNC Symbol;Acc:28666]

Sequence

>retro_opri_952
TGGGAAAGGAGTTCTCATTCTGGAAAGGATGCACCGAATGTTGAAGCAGGTGGAGACACAGACGTGATGCAGCAGGAGGC
AGCTCCAGTCTCTGCCCGGTCAAGGAAAACCAAACAGCCTAAAGAATGTTTGTTAATTCATCCAAAGACAACAAAAGAGG
GCGCCACCAAGACTAAGGAGAAAAGAAGAAAATCACTGATATTCTTGCAAAATCAGAGCCCAAACCAGGCACACCTGAGG
ATCTACAGAAGCTGATGAAGGACTAGTACAGCAGCAGTCGCTCAGTGATTGAATTAGAAGAACTGAACCTACCAGATTCT
TGTCTCCTCAAGGCCAATGATTTGACCCACAGACTTTCATCATACCTAAAAGAGATTTGTCCTAAGTGGGTAAAACTTTG
GAAAAACCACAGTGAGAATAAATCCGTCCTAATGCTGATCATCTGAAGCTCTGCCATCCCCACCCTGGAGCTCATTAGGT
CAATGACAGCATTTAAAGGAGACAGCAAAGTTACGAAATTATTTGCAAAACACATAAATGTCCAGGAACAAATGAAGTTG
CTGGAGAAGTGTGTGGTACACCTAGGTGTCGGGACTCCAGGAAGAATTAAAGAACTCGTTAATCAAGGTGGACTTAATTT
AAACCCCTTAAAGTTCCTGGTTTTTGACTGGAACTGAAGAGACCAGAAGCTAAGAAAAATGATGGACATTCCCGAGATAA
AAAAGGTGTTTGAACTTCTGGAAATGGAGTACTCAGTCAAAGCAAGTCTGAATCTTTGAAGTTGGGCCTGTTC

Alignment

ORF - retro_opri_952 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.29 %
• Parental protein coverage: 96.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WENQPAGAASSPASDVEAGGDTEVMQQETASVPAQSKKTKQPKECFLIQPKTTKEGGTKTKKRR-KKKIT
          WE.........P...VEAGGDT.VMQQE.A.V.A.S.KTKQPKEC.LI.PKTTKE.G....K...KKKIT
Retrocopy WERSSHSGKDAP--NVEAGGDTDVMQQEAAPVSARSRKTKQPKECLLIHPKTTKE-GATKTKEK<KKKIT

Parental  DILAKSEPKPGTPEDLQKLMKDYYSSIRSVIELEELNLPDSCFLKANDLTHSLSSYLKEICPKWVKLRKN
          DILAKSEPKPGTPEDLQKLMKD.YSS.RSVIELEELNLPDSC.LKANDLTH.LSSYLKEICPKWVKL.KN
Retrocopy DILAKSEPKPGTPEDLQKLMKD*YSSSRSVIELEELNLPDSCLLKANDLTHRLSSYLKEICPKWVKLWKN

Parental  HSEKKSVLMLIICSSAIRTLELIRSMTAFKGDSKVMKLFAKHIKVQEQIKLLEKRVVHLGVGTPGRIKEL
          HSE.KSVLMLII.SSAI.TLELIRSMTAFKGDSKV.KLFAKHI.VQEQ.KLLEK.VVHLGVGTPGRIKEL
Retrocopy HSENKSVLMLII*SSAIPTLELIRSMTAFKGDSKVTKLFAKHINVQEQMKLLEKCVVHLGVGTPGRIKEL

Parental  VKQGGLNLNPLKFLVFDWNWRDQKLRRMMDIPEIRKEVFELLEM-GVLSLCKSESLKLGLF
          V.QGGLNLNPLKFLVFDWN.RDQKLR.MMDIPEI.K.VFELLEM.GVLS..KSESLKLGLF
Retrocopy VNQGGLNLNPLKFLVFDWN*RDQKLRKMMDIPEIKK-VFELLEM<GVLSQSKSESLKLGLF

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_952 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009230	1 retrocopy	retro_cfam_1973,
Mustela putorius furo	ENSMPUG00000011324	2 retrocopies	retro_mputfur_1009, retro_mputfur_783,
Ochotona princeps	ENSOPRG00000002986	1 retrocopy	retro_opri_952 ,