RetrogeneDB ID: retro_opri_949

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_489:221188..222100(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DTWD1
• Ensembl ID: ENSOPRG00000002951
• Aliases: None
• Description: DTW domain containing 1 [Source:HGNC Symbol;Acc:30926]

Sequence

>retro_opri_949
ATGTCTCTCAACTCACCTATATTTCTCGAAGAAAGTGAAGAAAGTAATTCAAAATTTGTGGAAACAAAACAGTCACAGAC
TACTTCCATAGCTTCAGAAGATCCCCTTCAGAACTTATGTTTAGCATCTCAAGAAGTTCTTCATAAAGCTCAACAAACTG
GGAGATCAAAGTGTCTACGATGTGGTGGTTCCAGAATGTTTTACTGCTATACATGTTATGTCCCAGTTGAAAATGTACCT
ATTGAACAGATTCCACTTGTGAAGCTTCCATTGAAGATCGACATCATTAAACATCCAAATGAAACAGATGGCAAAAGTAC
TGCTATACATGCAAAACTCTTAGCACCTGATTTTGTGAACATTTATACATATCCTTGTATTCCAGAATATGAAGAACAGG
ATTATGAAGTTGCGCTTATTTTTCCTGGACCTCAGTCTGTCTCCATAAAAGATATCTCTTTCCATCTACAAAAACGAATG
CAAGATAATATTAGAGACAAAAGTGATGACCCTGATAAGCCAACTGTTAAACGTAAAAAAACTGAAGAAATGGAGGACCT
TGATTTGATTGGCAGCAAGGGCAAAGGCACAATACTGAAAAAAATTATTTTTATAGATAGCACTTGGAACCAGACAAACA
AAATATTCACTGATGAGAGACTTCAAGGATTGTTACAAGTTGAGTTGAAAACAAGAAAAACTTGCTTTTGGCGCCATCAA
AAAGGAAAGCCAGACACTTTCCTTTCCACAATTGAAGCAATTTACTACTTTCTTGTGGACTACCATACTGAAATACTAAA
AGAGAAATACACAGGACAATATGACAATCTTTTATTTTTCTACTCCTTTATGTACAGGCTGATAAAGGATGCCAAATGCT
CTGGAGATAAAGAAAAAAGAAAACTTATCCAT

Alignment

ORF - retro_opri_949 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLNSPVFLEESEESNSKFVETKQSQTTSIASEDPLQNLCLASQEVLYKAQQTGRSKCLRCGGSRMFYCY
          MSLNSP.FLEESEESNSKFVETKQSQTTSIASEDPLQNLCLASQEVL.KAQQTGRSKCLRCGGSRMFYCY
Retrocopy MSLNSPIFLEESEESNSKFVETKQSQTTSIASEDPLQNLCLASQEVLHKAQQTGRSKCLRCGGSRMFYCY

Parental  TCYVPVENVPIEQIPLVKLPLKIDIIKHPNETDGKSTAIHAKLLAPDFVNIYTYPCIPEYEEQDHEVALI
          TCYVPVENVPIEQIPLVKLPLKIDIIKHPNETDGKSTAIHAKLLAPDFVNIYTYPCIPEYEEQD.EVALI
Retrocopy TCYVPVENVPIEQIPLVKLPLKIDIIKHPNETDGKSTAIHAKLLAPDFVNIYTYPCIPEYEEQDYEVALI

Parental  FPGPQSVSIKDISFHLQKRMQDNIRDKSDDPDKPTVKRKKTEEMEGLDLIGSKGKGTILKKIIFIDSTWD
          FPGPQSVSIKDISFHLQKRMQDNIRDKSDDPDKPTVKRKKTEEME.LDLIGSKGKGTILKKIIFIDSTW.
Retrocopy FPGPQSVSIKDISFHLQKRMQDNIRDKSDDPDKPTVKRKKTEEMEDLDLIGSKGKGTILKKIIFIDSTWN

Parental  QTNKIFTDERLQGLLQVELKTRKTCFWRHQKGKPDTFLSTIEAIYYFLVDYHTEILKEKYTGQYDNLLFF
          QTNKIFTDERLQGLLQVELKTRKTCFWRHQKGKPDTFLSTIEAIYYFLVDYHTEILKEKYTGQYDNLLFF
Retrocopy QTNKIFTDERLQGLLQVELKTRKTCFWRHQKGKPDTFLSTIEAIYYFLVDYHTEILKEKYTGQYDNLLFF

Parental  YSFMYRLIKDAKCSGDKEKRKLIH
          YSFMYRLIKDAKCSGDKEKRKLIH
Retrocopy YSFMYRLIKDAKCSGDKEKRKLIH

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_949 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014926	1 retrocopy	retro_cfam_2081,
Cavia porcellus	ENSCPOG00000003461	2 retrocopies	retro_cpor_1476, retro_cpor_250,
Homo sapiens	ENSG00000104047	1 retrocopy	retro_hsap_2846,
Gorilla gorilla	ENSGGOG00000027921	1 retrocopy	retro_ggor_1973,
Nomascus leucogenys	ENSNLEG00000006167	1 retrocopy	retro_nleu_1598,
Otolemur garnettii	ENSOGAG00000013291	1 retrocopy	retro_ogar_499,
Ochotona princeps	ENSOPRG00000002951	2 retrocopies	retro_opri_136, retro_opri_949 ,
Pongo abelii	ENSPPYG00000006464	2 retrocopies	retro_pabe_2355, retro_pabe_2356,
Pan troglodytes	ENSPTRG00000007058	1 retrocopy	retro_ptro_1928,
Vicugna pacos	ENSVPAG00000008358	2 retrocopies	retro_vpac_509, retro_vpac_530,