RetrogeneDB ID: retro_itri_1378

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393466.1:1966010..1966694(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000022141
• Aliases: None
• Description: None

Sequence

>retro_itri_1378
GACCTTCTGGGACCCAGCCTTGAATATCTCTTCTGTTCAAGAAGATTCTCAATGAAAACTGTACCTGTGTTAGCTGACCA
GATGATCAGTAGAAGTGAATATGTGCATTCGAAAAATTTTATACAAGGAGGCATTAAGCTAGTGGATATTGGGCCGGCAC
TGTAAGAAGTTATTCCATATTGATTTGGGTTTGGCAAAAAATTATATAGACAACAAGACAAGGCAACACATACCACACAA
GATAAAATCCTCACTGGCACTGTCCACTATGCTAGCAGGAATGTACATCTTGGTATTGCGCAGTCACTGAGATGACATGG
AATCATTATGATATGTTTTGATGTATTTTAATAGAATTAGCTGCCATGGCAAGGACTAAAGGCTGCAATAAAGAAACAAA
TATATGAAAAGATTAGTGAAAAGATGATGTCCACTTCTAATGAAGTTTTAGATAAAGGGTTTCCTACAGAATTTACTGTG
TACTTAAATTATTGTAGTGGGCTGTTCTTTGAGGAAGCCCCTGATTACATGTATGTGAGGCAGCTATTCCACATCCTTTT
CAGTATCCTGAATCACCAATATGACTACAAGTTTGGCTGGACAATGTTAAAGCAAAGAGATGGATGGCAGGCAGCCTATC
CAGCAGACCCAAGCCCCCATAGGCAAGCAAACCGACAAAAGGAG

Alignment

ORF - retro_itri_1378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.87 %
• Parental protein coverage: 70.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFIHRDIKPDNFLMGIG-RHCNKLFLIDFG
          DLLGPSLE.LF..CSRRF.MKTV..LADQMISR.EYVH.KNFI...IK....L..IG.RHC.KLF.ID.G
Retrocopy DLLGPSLEYLF--CSRRFSMKTVPVLADQMISRSEYVHSKNFIQGGIK----LVDIG>RHCKKLFHIDLG

Parental  LAKKYRDNRTRQHIPYREDKNLTGTARYASINAHLGIEQSRRDDMESLGYVLMYFNRTS-LPWQGLKAAT
          LAK.Y.DN.TRQHIP......L......A..........S..DDMESL.YVLMYFNR.S.LPWQGLKAA.
Retrocopy LAKNYIDNKTRQHIPHKIKSSLALSTMLAGM--YILVLRSH*DDMESL*YVLMYFNRIS<LPWQGLKAAI

Parental  KKQKYEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEAPDYMYLRQLFRILFRTLNHQYDYTFDW
          KKQ.YEKISEK.MST..EVL.KGFP.EF..YLNYC.GL.FEEAPDYMY.RQLF.ILF..LNHQYDY.F.W
Retrocopy KKQIYEKISEKMMSTSNEVLDKGFPTEFTVYLNYCSGLFFEEAPDYMYVRQLFHILFSILNHQYDYKFGW

Parental  TMLKQKAAQQAASSSGQGQQAQTPTGKQ
          TMLKQ....QAA.........Q....K.
Retrocopy TMLKQRDGWQAAYPADPSPHRQANRQKE

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_1378 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1378 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 16 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005326	2 retrocopies	retro_btau_1662, retro_btau_49,
Canis familiaris	ENSCAFG00000018286	1 retrocopy	retro_cfam_1887,
Callithrix jacchus	ENSCJAG00000021121	1 retrocopy	retro_cjac_2680,
Homo sapiens	ENSG00000113712	1 retrocopy	retro_hsap_32,
Gorilla gorilla	ENSGGOG00000013926	3 retrocopies	retro_ggor_1178, retro_ggor_742, retro_ggor_984,
Myotis lucifugus	ENSMLUG00000002910	4 retrocopies	retro_mluc_1531, retro_mluc_2134, retro_mluc_2215, retro_mluc_597,
Macaca mulatta	ENSMMUG00000001758	2 retrocopies	retro_mmul_2207, retro_mmul_295,
Monodelphis domestica	ENSMODG00000009937	1 retrocopy	retro_mdom_2005,
Oryctolagus cuniculus	ENSOCUG00000006669	7 retrocopies	retro_ocun_1068, retro_ocun_1098, retro_ocun_1506, retro_ocun_500, retro_ocun_502, retro_ocun_506, retro_ocun_644,
Otolemur garnettii	ENSOGAG00000003253	2 retrocopies	retro_ogar_1195, retro_ogar_825,
Sorex araneus	ENSSARG00000011446	1 retrocopy	retro_sara_518,
Sarcophilus harrisii	ENSSHAG00000015356	1 retrocopy	retro_shar_834,
Sus scrofa	ENSSSCG00000014435	1 retrocopy	retro_sscr_560,
Ictidomys tridecemlineatus	ENSSTOG00000011492	1 retrocopy	retro_itri_1674,
Ictidomys tridecemlineatus	ENSSTOG00000022141	1 retrocopy	retro_itri_1378 ,
Drosophila melanogaster	FBgn0015024	4 retrocopies	retro_dmel_10, retro_dmel_32, retro_dmel_40, retro_dmel_67,