RetrogeneDB ID: retro_itri_257

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:3702082..3702713(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000015459
• Aliases: None
• Description: None

Sequence

>retro_itri_257
ACAATGGAACTGGCTGACCTGGAACCCCTGCTAGAAGAGTAGGGCAAACTGACAATTACCAAACCAACCAAAGCTGAGGA
AGAACAAACATACTCAAGAGTCCCAGGATGAAGAGGAGGTTGTGTGGTACTGATGCTTTCCCTGCAAGTGCACTGTGCCA
AGGAGATGGAGGAATTGGTGTATAAGGTCTGGTAGGGATGTGTGAGGGTCATCCCATATGATTTGCTCCTTGACTGATTG
AAGGACAATGACTACCTGCTCACAGCCATAGAACACATGTGCCCTCCTTTCAGGCTTGCTTCAAGATCATCTTCTGCATC
TATACAGAAACTTGAAAACTTTTGGACCCATCTGCTTGATTGTGCACTTTGACTTTTTTTGGGAATACTGACCACACTCA
AATTTATTTATTTCATAGCTACTCTTCAGGAGAAGGCAGTTTGGGTGATTTTCTTTTTGGGTGCAGTGATCTGCTGCAGC
TTTTCCTGGCTCTTCCAACATCATCTTTTGTCAAAATCAGACTTTTTTCAAACAAGACTATTAAGAGATTGTTCAACCGA
TTATGGGAAGCTTTGTTTCTTGGCTCTAGTACATCTTCTACTGCTTCCCACAGTGTGGACTAACTCAACTC

Alignment

ORF - retro_itri_257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.18 %
• Parental protein coverage: 57.6 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SVELAELGPLLEEKGKRVIANPNKAEEEQT-CPVPQEEEEEVR-VLTLPLQAHHAMEKMEEFVYKVWEGR
          ..ELA.L.PLLEE.GK..I..P.KAEEEQT.....Q.EEE.V..VL.L.LQ.H.A.E.MEE.VYKVW.G.
Retrocopy TMELADLEPLLEE*GKLTITKPTKAEEEQT>TQESQDEEEVVW<VLMLSLQVHCAKE-MEELVYKVW*GC

Parental  WRVIPYDVLPDWLKDNDYLL-HGHRPPMPSFRACFKSIFRIHTET-GNIWTHLLGFVLFLFLGILTMLRP
          .RVIPYD.L.D.LKDNDYLL.H.HR...PSF.ACFK.IF.I.TET..N.WTHLL...L.LFLGILT.L..
Retrocopy VRVIPYDLLLD*LKDNDYLL<HSHRTHVPSFQACFKIIFCIYTET>ENFWTHLLDCAL*LFLGILTTLK-

Parental  NMYFMAPLQEKVVFGMFFLGAVLCLSFSWLF-HTVYCHSEKVSRTFSKLDYSGIALLIMGSFVPWLYYSF
          ..YF.A.LQEK.V...FFLGAV.C.SFSWLF.....C.......TF.K.DY..I...IMGSFV.WL.Y.F
Retrocopy FIYFIATLQEKAVWVIFFLGAVICCSFSWLF>NIIFCQNQ----TFFKQDY*EIVQPIMGSFVSWL*YIF

Parental  YCSPQPRLIYL
          YC.PQ..L..L
Retrocopy YCFPQCGLTQL

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_257 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_257 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 20 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012199	1 retrocopy	retro_amel_1853,
Choloepus hoffmanni	ENSCHOG00000006450	8 retrocopies	retro_chof_1127, retro_chof_1222, retro_chof_1917, retro_chof_2218, retro_chof_2380, retro_chof_471, retro_chof_749, retro_chof_995,
Callithrix jacchus	ENSCJAG00000006268	3 retrocopies	retro_cjac_2262, retro_cjac_740, retro_cjac_741,
Cavia porcellus	ENSCPOG00000000482	1 retrocopy	retro_cpor_470,
Dipodomys ordii	ENSDORG00000006876	1 retrocopy	retro_dord_19,
Felis catus	ENSFCAG00000013565	1 retrocopy	retro_fcat_1514,
Loxodonta africana	ENSLAFG00000003520	1 retrocopy	retro_lafr_277,
Macropus eugenii	ENSMEUG00000015439	1 retrocopy	retro_meug_516,
Microcebus murinus	ENSMICG00000007942	3 retrocopies	retro_mmur_1199, retro_mmur_184, retro_mmur_764,
Myotis lucifugus	ENSMLUG00000016102	2 retrocopies	retro_mluc_1275, retro_mluc_200,
Macaca mulatta	ENSMMUG00000007046	1 retrocopy	retro_mmul_1322,
Mustela putorius furo	ENSMPUG00000011215	1 retrocopy	retro_mputfur_550,
Otolemur garnettii	ENSOGAG00000033821	4 retrocopies	retro_ogar_1558, retro_ogar_1624, retro_ogar_2838, retro_ogar_783,
Ochotona princeps	ENSOPRG00000004528	3 retrocopies	retro_opri_101, retro_opri_1050, retro_opri_392,
Pongo abelii	ENSPPYG00000000342	1 retrocopy	retro_pabe_1072,
Sorex araneus	ENSSARG00000007680	1 retrocopy	retro_sara_25,
Ictidomys tridecemlineatus	ENSSTOG00000015459	3 retrocopies	retro_itri_215, retro_itri_257 , retro_itri_512,
Tupaia belangeri	ENSTBEG00000015149	2 retrocopies	retro_tbel_1501, retro_tbel_1804,
Tarsius syrichta	ENSTSYG00000001491	1 retrocopy	retro_tsyr_125,
Tursiops truncatus	ENSTTRG00000006381	2 retrocopies	retro_ttru_1055, retro_ttru_863,