RetrogeneDB ID: retro_opri_737

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_27070:42462..43354(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNW1
• Ensembl ID: ENSOPRG00000007568
• Aliases: None
• Description: SNW domain containing 1 [Source:HGNC Symbol;Acc:16696]

Sequence

>retro_opri_737
ACGATTGTAAAGGAATAAGAATAAAAGATTCTTTCCTGTATTTCCAACTGGAAAAACATAAAAGCTTAGATAATTCTATT
GGAAAAATGTCTTGCAGCTGTAGGGAGAGGGCTACATTTATTAGACACATACATGAAAATTTTGGGAAAACTGGCTGAAG
CTGTCTACATTGCCAATCAGAAGGCTTGAGAAGTTGTACAGATACATGCCCAAGTTGAGAGGAAGATGGCACAAAAAGAA
AAGGAGAAACATGAAGAACAATTAACAGAAATGTCCTGGAAAACTAGGGAGGAGAGAGCAGGGATCAAAACCCCTATGGA
TGAAGACCTGGGGAGGCACATGAATGGGATGAAATCCAGCATGACAGATGAGAGGAGGGGCAGCACCAGCAGAATCTCTC
CAGGCCTGCTCCTGAGAGGAGCTCAAAACTACAGAGAAATGAAAATCAGGGTCTCAATGAAGGCATTGCTGTTAGTGTGT
CTGGTCTCATACTTCCAATGAACGTCAGGATGACCAAAGGTTTTTCAACCAGTCCAAGGGTCCGGACAGTGGATTTGCAG
TTGGAGAGGATGAAATTTACAATGCTTATAATCAAGCCTGGAGGGGAGGTAAAGATATACCCTGGAGTGTTTTACAGGCC
AAGTAAAAATCTGGACGACATGTATGGTGATGATCCAGAAGCCAGAATAAAGACCAAACTCCCGACAAGGAGTTTTCTGG
TCCAGACAATAGGCAGAGAGGCCGGAAAGGACCAGTTCAGTTTGAGGAAGACCTGTTTGGTTTGGACAAATTTTTGAAAG
AAGCCAAGCAGTATGTATGGTGGCTCCAGAAGACCTTTAATAGCAGCCACCCCAAGGAGCATGAACATGAAAGCACAAAG
ATGAGAAAGGAG

Alignment

ORF - retro_opri_737 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.62 %
• Parental protein coverage: 55.78 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVH-INENFAKLAEALYIADRKAREAVETRA
          T.....E.KI..CISNWKN.K...I.L.K.LAA.GRGL...........KLAEA.YIA..KA.E.V...A
Retrocopy TIVKE*E*KILSCISNWKNIKA*IILLEKCLAAVGRGLHLLDTYMKILGKLAEAVYIANQKA*EVVQIHA

Parental  QVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKE-DGEARERDEIRHDRRKERQHDRNLSRAAPD
          QVERKMAQKEKEKHEE.L.EM..K.RE.RAGIKT.......GEA.E.DEI.HDR..E.QH..NLSR.AP.
Retrocopy QVERKMAQKEKEKHEEQLTEMSWKTREERAGIKTPMDED<PGEAHEWDEIQHDR*EEGQHQQNLSRPAPE

Parental  KRSKLQRNENRDISEVIALGVPN-PRTSNEVQYDQRLFNQSKGMDSGFAGGEDEIYNVYDQAWRGGKDMA
          ..SKLQRNEN....E.IA..V.....TSNE.Q.DQR.FNQSKG.DSGFA.GEDEIYN.Y.QAWRGGKD..
Retrocopy RSSKLQRNENQGLNEGIAVSVSG<SHTSNERQDDQRFFNQSKGPDSGFAVGEDEIYNAYNQAWRGGKDIP

Parental  QSI-YRPSKNLDKDMYGDDLESKIKTNRFVPDKEF-SGSDRRQRGREGPVQFEEDPFGLDKFLEEAKQH-
          .S..YRPSKNLD.DMYGDD.E..IKT....P...F.SG.D.RQRGR.GPVQFEED.FGLDKFL.EAKQ..
Retrocopy WSV>YRPSKNLD-DMYGDDPEARIKTK--LPTRSF<SGPDNRQRGRKGPVQFEEDLFGLDKFLKEAKQYV

Parental  GGSKRPSDSSRPKEHEHESKKRRKE
          ........SS.PKEHEHES.K.RKE
Retrocopy WWLQKTFNSSHPKEHEHESTKMRKE

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_737 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 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003976	2 retrocopies	retro_amel_163, retro_amel_912,
Canis familiaris	ENSCAFG00000030409	1 retrocopy	retro_cfam_195,
Callithrix jacchus	ENSCJAG00000016947	2 retrocopies	retro_cjac_2932, retro_cjac_576,
Dipodomys ordii	ENSDORG00000012380	3 retrocopies	retro_dord_693, retro_dord_781, retro_dord_782,
Felis catus	ENSFCAG00000001637	1 retrocopy	retro_fcat_635,
Homo sapiens	ENSG00000100603	1 retrocopy	retro_hsap_174,
Gorilla gorilla	ENSGGOG00000026016	1 retrocopy	retro_ggor_257,
Loxodonta africana	ENSLAFG00000003482	2 retrocopies	retro_lafr_474, retro_lafr_787,
Myotis lucifugus	ENSMLUG00000005228	2 retrocopies	retro_mluc_387, retro_mluc_805,
Monodelphis domestica	ENSMODG00000005252	1 retrocopy	retro_mdom_1841,
Mustela putorius furo	ENSMPUG00000008724	1 retrocopy	retro_mputfur_551,
Mus musculus	ENSMUSG00000021039	2 retrocopies	retro_mmus_1022, retro_mmus_387,
Nomascus leucogenys	ENSNLEG00000016771	1 retrocopy	retro_nleu_982,
Ochotona princeps	ENSOPRG00000007568	1 retrocopy	retro_opri_737 ,
Pongo abelii	ENSPPYG00000006031	1 retrocopy	retro_pabe_454,
Pan troglodytes	ENSPTRG00000006587	1 retrocopy	retro_ptro_165,
Sorex araneus	ENSSARG00000002279	3 retrocopies	retro_sara_403, retro_sara_568, retro_sara_727,
Taeniopygia guttata	ENSTGUG00000012340	2 retrocopies	retro_tgut_15, retro_tgut_30,
Tarsius syrichta	ENSTSYG00000010951	1 retrocopy	retro_tsyr_1871,