RetrogeneDB ID: retro_itri_106

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393332.1:3206956..3207919(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000002090
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EPCAM
• Ensembl ID: ENSSTOG00000008631
• Aliases: None
• Description: epithelial cell adhesion molecule [Source:HGNC Symbol;Acc:11529]

Sequence

>retro_itri_106
ATGGCCAGGGGCCCCGGCCTCGCGCCACCTCCGCTGCTGGCACTGCTGGTGCTGGCGGCGGTGTCTGGCTACGCTGTCGC
GCAGTACAACTGCACATGCCCCACCAACAAGATGACCGTGTGCTCCCAGGATGGCCCTGGGGGCCGCTGCCAATGCCGCG
CGCTCGGCTCGGGCGTGGTGGTCGACTGCTCCAAGCTGACCTCCAAGTGCCTGCTGCTCAAGGCCCGCATGAGCATCCCT
AAGAGCGGTCGTCGACTGGTGCGGCCGAACGAGCACGCGATCTTGGACAATGATGGCCTCTACGACCCCGAATGTGACCA
CGAGGGCCGCTTCAAGGCGCGCCAGTGCAACCAGACGTCGGTGTGCTGGTGCGTGAACTCGGTGGGTGTGCGCCGTACGG
ACAAGGGCGACCAGAGCCTGCGCTGCGATGAGGTGGTGCGTACCCACCACATCCTCATTGACATGCGCCACCGCGCGACC
GACCGCGCCTTCAACCACTCCGACCTGGACACCGAGCTGCGGCGGCTCTTCCGCGAGCGCTATCAGCTGCACCCCAGGTT
CCTGACGGCTGTGCACTATGAGGAACCTACCATTCAGATCGAGCTGTGGCAGAACGCCTCGCAGAAAGTCCCCGGCGACG
TGGACATAGCTGACGCCGCCTACTACTTTGAGAGAGATATCAAGGGCGAGTCGCTGTTCGCGGGCCCAGGAGGCCTGGAC
ATGCAGGTGCGCGGTGAGCCTCTGCACGTGGAGCAGACGCTCATCTATTACCTGGACGAGAAGCCTCCCCAATTCTCCAT
GAAGCGCCTCACCGCCGGCCTCATCGCCGTCATCGTGGTGGTCGTGGTAGCCTTGGTCGCTGGCCTGGTTGTCCTGGTGA
TCACCAACCGGAGGAAGTCCGGGAAGTATAAGAAGGTGGAGATCAAAGAACTGGGGGAGTTGAGAAATGAACCCAGCTTG
TAG

Alignment

ORF - retro_itri_106 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.61 %
• Parental protein coverage: 84.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KCSSIGTKNTVICSKLASKCLVMKAEMNSSKSGRR-GKP-EGAIQNNDGLYDPDCDEKGLFKAKQCNGTA
          .C...G....V.CSKL.SKCL..KA.M...KSGRR...P.E.AI..NDGLYDP.CD..G.FKA.QCN.T.
Retrocopy QCRALGSGVVVDCSKLTSKCLLLKARMSIPKSGRRLVRPNEHAILDNDGLYDPECDHEGRFKARQCNQTS

Parental  TCWCVNTAGVRRTDK-DTEITCSERVRTFWIMIELKHKAREKPYNVQSLQTAIQEMMTTRYLLDPKFITN
          .CWCVN..GVRRTDK.D....C.E.VRT..I.I...H.A.....N...L.T........RY.L.P.F.T.
Retrocopy VCWCVNSVGVRRTDKGDQSLRCDEVVRTHHILIDMRHRATDRAFNHSDLDTELRRLFRERYQLHPRFLTA

Parental  ILYENNVITIDLVQNSSQKTQNDVDIADVAYYFEKDVKGESLFR-TSKIDLRVDGEQLELDPGQTLIYYV
          ..YE...I.I.L.QN.SQK...DVDIAD.AYYFE.D.KGESLF......D..V.GE.L.....QTLIYY.
Retrocopy VHYEEPTIQIELWQNASQKVPGDVDIADAAYYFERDIKGESLFAGPGGLDMQVRGEPLHVE--QTLIYYL

Parental  DEKAPEFSMQGLKAGIIAVIVVVTIAVIAGIVVLVISRRKKTTKYEKAEIKEMGEMHRELS
          DEK.P.FSM..L.AG.IAVIVVV..A..AG.VVLVI..R.K..KY.K.EIKE.GE...E.S
Retrocopy DEKPPQFSMKRLTAGLIAVIVVVVVALVAGLVVLVITNRRKSGKYKKVEIKELGELRNEPS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_106 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_106 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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,