RetrogeneDB ID: retro_opri_252

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4235:40015..40828(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000006805
• Aliases: None
• Description: None

Sequence

>retro_opri_252
CCTTTCCAGCTCACTGTGCAAAAGCTGGAGCAAGCCATGGTTGAAGCTAGACTCAAGGGGAAAAGAGTCAAAGGCCTCGT
GCTAATCAACCCACAGAATCCTCTGGGTGGCATCTACTCCCAAGAGTCACTGAAGGAATACCTGGAATTTGCCAAGAGGA
ATTACTTGCATGTGATCATGGATGAGATTTACATGCTCACTGTGTTTGATGACTCTCTCAAGTTCCACAGCGTGCTGAGC
ATAGAAAGCTTGCCTGACCCCAACAGGACCCACGTGATCTGGGGAACTAGTAAGGATTTTGGCATCTCTGGCTTCCGCTT
TGGTGCTCTGTACACCCACAACAAGGATGTGGCCTCTGCCGTGTGCTCCTTTGGCTACCTCCACGGTACCTCTGGCACCG
CCCAGTACAAACTACACCGCCTGCTCCAAGACACAGAATGGATCAACACAGTGTACCTGCCGACTAACCTCTCATGGCTC
AGGAAGGCCTACAATTATGTCACTGGTCAGCTGAAGCTATTGGGAATCCCCTTTCTCAGTGGTGGCTCTGGCCTCTACAT
CTGGATCAACTTGAAGTCGTACCTAGAACCATGTACATTTGATGAAGAACTGGCCCTCCATCAGCACTTTCTGGACATGA
AGGTGATGTTATCCCGTGGCAAAAGCTTCAAATGTAAAGAGCCTGGCTGGTTCCGCCTCATGTTTGCAGAAAAGCTTCCA
GTGCTGGAAGTGGCCATGCAACGGTTGCACAACGCGTTACAGATTTAGAAACAGATTCAGGAACAGAAACAGATAGAGAA
GATGCTGGTGGAT

Alignment

ORF - retro_opri_252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.1 %
• Parental protein coverage: 77.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PFQLK-KNWEQAMGEARFWGKRVKGLVLVNPQNPLGGIYSQESLKEYLEFAKRNYLHVIMDEIYMLTVFD
          PFQL.....EQAM.EAR..GKRVKGLVL.NPQNPLGGIYSQESLKEYLEFAKRNYLHVIMDEIYMLTVFD
Retrocopy PFQLTVQKLEQAMVEARLKGKRVKGLVLINPQNPLGGIYSQESLKEYLEFAKRNYLHVIMDEIYMLTVFD

Parental  DSLKFHSVLSIKSLPDPNRTHVIWGTSKDFGISGFRFGALYTHNKDVASAVCSFGYLHSTSGTAQYKLHR
          DSLKFHSVLSI.SLPDPNRTHVIWGTSKDFGISGFRFGALYTHNKDVASAVCSFGYLH.TSGTAQYKLHR
Retrocopy DSLKFHSVLSIESLPDPNRTHVIWGTSKDFGISGFRFGALYTHNKDVASAVCSFGYLHGTSGTAQYKLHR

Parental  LLQDTEWINTVYLPTNLSRLRKAYNYVTGQLKLLGIPFLSGGAGLYIWINLKSYLEPCTFDEELALHQHF
          LLQDTEWINTVYLPTNLS.LRKAYNYVTGQLKLLGIPFLSGG.GLYIWINLKSYLEPCTFDEELALHQHF
Retrocopy LLQDTEWINTVYLPTNLSWLRKAYNYVTGQLKLLGIPFLSGGSGLYIWINLKSYLEPCTFDEELALHQHF

Parental  LDMKVMLSRGKSFKCKEPGWFRLMFAEKLPTLEVAMQRLHNALQIQKQIQEQKQIEKMLAD
          LDMKVMLSRGKSFKCKEPGWFRLMFAEKLP.LEVAMQRLHNALQI.KQIQEQKQIEKML.D
Retrocopy LDMKVMLSRGKSFKCKEPGWFRLMFAEKLPVLEVAMQRLHNALQI*KQIQEQKQIEKMLVD

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_252 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 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011384	1 retrocopy	retro_cjac_100,
Dipodomys ordii	ENSDORG00000005058	1 retrocopy	retro_dord_340,
Equus caballus	ENSECAG00000011908	1 retrocopy	retro_ecab_575,
Echinops telfairi	ENSETEG00000009026	2 retrocopies	retro_etel_1006, retro_etel_204,
Homo sapiens	ENSG00000205126	1 retrocopy	retro_hsap_3553,
Myotis lucifugus	ENSMLUG00000005151	1 retrocopy	retro_mluc_1235,
Nomascus leucogenys	ENSNLEG00000017966	1 retrocopy	retro_nleu_2326,
Ochotona princeps	ENSOPRG00000002097	1 retrocopy	retro_opri_526,
Ochotona princeps	ENSOPRG00000006805	7 retrocopies	retro_opri_1064, retro_opri_1151, retro_opri_251, retro_opri_252 , retro_opri_398, retro_opri_399, retro_opri_808,
Pongo abelii	ENSPPYG00000003340	1 retrocopy	retro_pabe_2934,
Pan troglodytes	ENSPTRG00000028662	1 retrocopy	retro_ptro_2414,
Tupaia belangeri	ENSTBEG00000016623	1 retrocopy	retro_tbel_3677,
Tursiops truncatus	ENSTTRG00000002727	1 retrocopy	retro_ttru_1321,