RetrogeneDB ID: retro_opri_1225

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_9960:8995..9803(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000003193
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EPCAM
• Ensembl ID: ENSOPRG00000004301
• Aliases: None
• Description: epithelial cell adhesion molecule [Source:HGNC Symbol;Acc:11529]

Sequence

>retro_opri_1225
TGCCAGTGCCGCGCGCTCGGCTCGAACACCGTGGTGGACTGCTCCACGCTGACCTCCAAGTGCCTGCTGCTCAAGGCGCG
TATGAGTAATACCAAGAGCGGCCGCGGGCTAGTCCGGCCGAGCGAGCACGCGATCGTGGACAACGACGGCCTCTACGACC
CCGACTGCGACCAAGAAGGTCGCTTCAAGGCGCGCCAGTGCAACCAGACCTCGGTGTGCTGGTGCGTGAACTCGGTGGGC
GTGCGCCGCACCGACAAGGGCGACCAGAACCTGCGCTGCGACGAGCTTGTGCGCACGCACCACATCCTCATCGACCTGCG
CCACCGGCCGGCTGCGCGCGCCTTCAACCACTCGGAGCTGGACGCCGCGCTGCGCCGCCTCTTCCGCGAGCGCTACCGGC
TGCAGCCCCGCTTCGTGGAGGCGGTGCACTACGAGGAGCCCACCATCCAGATCGAGCTGCAACAGAACGCTTCGCAGAAG
GCCCCCCGGCGACGTGGACATCGCCCGACGCCGCCTACTACTTCGAGAGGGACATCAAGGGGCGAGTCGCTCTTCGCTGG
CAGCGGTGACATGGCCGTACAGGTGCGCGGTGAGCCCCTGCACGTGGAGCGCACGCTCATCTACTACCTGGACGAGCAGC
CGCCCCCAGTTCTCCATGAAGCGCCTCACCTCCGGTCTCATCGCCGTCATCGTGGTGGTGGTGCTGGCCGTCATCGCCGG
CCTGGTGGTCCTGGTGGTCAGCAACCGCAGGAAGTCGGGGAAGTACAGGAAGGTGGAGATCAAGGAGATGGGGGAGTTGA
GAAATGAG

Alignment

ORF - retro_opri_1225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.65 %
• Parental protein coverage: 86.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CQCTSIGSQSTVLCSKLASKCLVMKAEMTSSKSGRR-AKP-EGAIQNNDGLYDPDCDEQGLFKAKQCNGT
          CQC...GS...V.CS.L.SKCL..KA.M...KSGR....P.E.AI..NDGLYDPDCD..G.FKA.QCN.T
Retrocopy CQCRALGSNTVVDCSTLTSKCLLLKARMSNTKSGRGLVRPSEHAIVDNDGLYDPDCDQEGRFKARQCNQT

Parental  ATCWCVNTAGVRRTDK-DTEITCPERVRTYWIIIELKHKERQKPYDTQSLRKAIEQLITSRYLLDPKFIT
          ..CWCVN..GVRRTDK.D....C.E.VRT..I.I.L.H...........L..A...L...RY.L.P.F..
Retrocopy SVCWCVNSVGVRRTDKGDQNLRCDELVRTHHILIDLRHRPAARAFNHSELDAALRRLFRERYRLQPRFVE

Parental  DILYENNVITIDLMQNSSQKT-QNDVDIA-DVAYYFEKDVK-GESLIQSSNKMELTVNGEPVELDPGQTL
          ...YE...I.I.L.QN.SQK....DVDIA.D.AYYFE.D.K.GESL...S..M...V.GEP.......TL
Retrocopy AVHYEEPTIQIELQQNASQKA>PGDVDIA>DAAYYFERDIK>GESLFAGSGDMAVQVRGEPLHVE--RTL

Parental  IYYVDEK-APEFSMQGLKAGIIAVIVVVVLAVIAGIVVLVMSRKKRNAKYEKAEVKEMGEMHRE
          IYY.DE...P.FSM..L..G.IAVIVVVVLAVIAG.VVLV.S......KY.K.E.KEMGE...E
Retrocopy IYYLDEQ>RPQFSMKRLTSGLIAVIVVVVLAVIAGLVVLVVSNRRKSGKYRKVEIKEMGELRNE

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_1225 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 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006474	1 retrocopy	retro_btau_66,
Choloepus hoffmanni	ENSCHOG00000013834	1 retrocopy	retro_chof_258,
Callithrix jacchus	ENSCJAG00000000624	1 retrocopy	retro_cjac_3006,
Dasypus novemcinctus	ENSDNOG00000011799	1 retrocopy	retro_dnov_345,
Erinaceus europaeus	ENSEEUG00000009462	1 retrocopy	retro_eeur_151,
Macropus eugenii	ENSMEUG00000015074	2 retrocopies	retro_meug_1984, retro_meug_474,
Microcebus murinus	ENSMICG00000000151	1 retrocopy	retro_mmur_739,
Macaca mulatta	ENSMMUG00000012390	1 retrocopy	retro_mmul_34,
Monodelphis domestica	ENSMODG00000001077	1 retrocopy	retro_mdom_104,
Mus musculus	ENSMUSG00000045394	1 retrocopy	retro_mmus_185,
Ochotona princeps	ENSOPRG00000004301	1 retrocopy	retro_opri_1225 ,
Pelodiscus sinensis	ENSPSIG00000015680	1 retrocopy	retro_psin_22,
Pan troglodytes	ENSPTRG00000011902	1 retrocopy	retro_ptro_92,
Rattus norvegicus	ENSRNOG00000015667	1 retrocopy	retro_rnor_252,
Sus scrofa	ENSSSCG00000008429	1 retrocopy	retro_sscr_69,
Ictidomys tridecemlineatus	ENSSTOG00000008631	1 retrocopy	retro_itri_106,
Tursiops truncatus	ENSTTRG00000004235	2 retrocopies	retro_ttru_21, retro_ttru_394,