RetrogeneDB ID: retro_itri_697

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393312.1:2080412..2081206(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT19
• Ensembl ID: ENSSTOG00000014403
• Aliases: None
• Description: keratin 19 [Source:HGNC Symbol;Acc:6436]

Sequence

>retro_itri_697
TCAGGCAAATACAGCCATTATTTTACGACCACTGAGGACCTAAGAGCCAAAATTCTTGGTGCAACCATTGAGACTTCCAG
GATCAGTCTTCAGATCAGCAATGTGTGTTTGGCTACAGTTGACTTCCAAAACAAGTTTGACATGGAGCAAGCTCTGCATC
TGAGCACAGAAGCCAACTTCAATGGCCTTGAATGATGCTGGACAAGCTGACTCTGGGTAGAATCCACCTCAAGGAGAAAT
TATAACACAGGAAGGATGAGTTGGCCTATCTGAAAAGAAATCATGAGAAGGAACTAAGTATCTTGAGGGATCAGATGCGT
GCAGATGTTAATTTTGCTCCTGGCATGGTCATAACTAAGATCCTGAGTGATATGAGAGACCAATATGAGATCATACCTGA
AAAGAACTGGAAAAACATTGAACACTAGCTCAATAGCTAGACCCAGGAATTGAATCTGGAAGTCACAGGCCACATGGAAC
AGATACAGTTGAACAATTCAGGAGATAGGCAGAATATCTTCTAGAGTCTTGAGATGGAGCCACAATTACAGTTCTGCAAG
AAAATTGCCCTGCAAGACATGCTGACAAACAGGGATGTCTACTTCTAGGCCCAGAAGATACAAGTTCAAGTGATGATGAG
TATCACTTGAAGCTGAGCTAGGTGACATGCATGCTAACACCAATAACAGAACCAAGAGAACCAGCAGCTCATAAACATTA
ATTCATGACTGGAGCAGATTGCCACCTACTGAAGCCTGCTCTAGGGCCAGGACACCCAGTACAATAATCTACCC

Alignment

ORF - retro_itri_697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.64 %
• Parental protein coverage: 68.51 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SRDYSHYFKTIEDLRDKILGATIENSKIVLQIDNARLAADDFRTKFETEQALRLSVEADINGLR-RVLDE
          S..YSHYF.T.EDLR.KILGATIE.S.I.LQI.N..LA..DF..KF..EQAL.LS.EA..NGL....LD.
Retrocopy SGKYSHYFTTTEDLRAKILGATIETSRISLQISNVCLATVDFQNKFDMEQALHLSTEANFNGLE<MMLDK

Parental  LTLARTDLEMQIEGLKEELAYLKKNHEEEISALRGQVGGQVNVEVDSTPGIDLAKILNDMRSQYEVMAEK
          LTL.R..L.......K.ELAYLK.NHE.E.S.LR.Q....VN......PG....KIL.DMR.QYE...EK
Retrocopy LTLGRIHLKEKL*HRKDELAYLKRNHEKELSILRDQMRADVNF----APGMVITKILSDMRDQYEIIPEK

Parental  NRKDAEAWFTSRTEELNREVAGHSEQLKMSESEVTDLRRTLQGLEIELQSQLSMKAALEGTLAETEARYG
          N.K..E....S.T.ELN.EV.GH.EQ.....S...D.......LE.E.Q.Q...K.AL...L........
Retrocopy NWKNIEH*LNS*TQELNLEVTGHMEQIQLNNS--GDRQNIF*SLEMEPQLQFCKKIALQDMLTNRDVYF*

Parental  ARLAQIQARIS-SIEAQLGDVRADTER-QNLEYQQLMDIKSRLEQEIATYRSLLEGQDAHYNNLP
          A...Q.Q...S.S.EA.LGD..A.T...QN.E.QQL..I.S.LEQ.IATY.SLL.GQD..YNNLP
Retrocopy AQKIQVQVMMS>SLEAELGDMHANTNN<QNQENQQLININS*LEQ-IATY*SLL*GQDTQYNNLP

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_697 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_697 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 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000029756	9 retrocopies	retro_cjac_1151, retro_cjac_1812, retro_cjac_2347, retro_cjac_2646, retro_cjac_3108, retro_cjac_3198, retro_cjac_3237, retro_cjac_3358, retro_cjac_633,
Equus caballus	ENSECAG00000014086	2 retrocopies	retro_ecab_76, retro_ecab_931,
Echinops telfairi	ENSETEG00000007881	6 retrocopies	retro_etel_1217, retro_etel_1319, retro_etel_191, retro_etel_480, retro_etel_685, retro_etel_95,
Homo sapiens	ENSG00000171345	3 retrocopies	retro_hsap_3486, retro_hsap_585, retro_hsap_959,
Gorilla gorilla	ENSGGOG00000016901	3 retrocopies	retro_ggor_2352, retro_ggor_518, retro_ggor_773,
Macropus eugenii	ENSMEUG00000016158	3 retrocopies	retro_meug_1860, retro_meug_403, retro_meug_826,
Macaca mulatta	ENSMMUG00000018653	4 retrocopies	retro_mmul_1770, retro_mmul_717, retro_mmul_774, retro_mmul_790,
Nomascus leucogenys	ENSNLEG00000010787	3 retrocopies	retro_nleu_1609, retro_nleu_2204, retro_nleu_800,
Oryctolagus cuniculus	ENSOCUG00000016132	1 retrocopy	retro_ocun_1884,
Otolemur garnettii	ENSOGAG00000024306	1 retrocopy	retro_ogar_1301,
Ochotona princeps	ENSOPRG00000007908	2 retrocopies	retro_opri_337, retro_opri_673,
Pongo abelii	ENSPPYG00000008416	3 retrocopies	retro_pabe_2880, retro_pabe_603, retro_pabe_820,
Pan troglodytes	ENSPTRG00000009168	3 retrocopies	retro_ptro_2074, retro_ptro_2359, retro_ptro_430,
Ictidomys tridecemlineatus	ENSSTOG00000014403	2 retrocopies	retro_itri_1514, retro_itri_697 ,