RetrogeneDB ID: retro_itri_535

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393299.1:9281907..9282906(-)
• Located in intron of: ENSSTOG00000021519

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000000014
• Aliases: None
• Description: None

Sequence

>retro_itri_535
TCGGAGATGGCGACCGTGAAGGGGGAGCTCTTCAAGAATTTGGCTCCCGAGGAGCGCGTCCACCACACCAAGGTGTCCAT
TATAGGGAGCGGGTCGGTGGGCGTGGCCTGCGCCTTAAGCATCTTGCTGAAAGGCCTGAGCGACGAGCTCGCCCTCGTGG
ATGTTAACGAAGCCAGGCTGAAGGGCGAGACCCTGGACCTTCAGCAAGGCAGCGCCTTCGCGAAGCTGCCCAGCATCGTG
TGCAGCAGAGACTACCTGGTCACCGCCGACTCCAGCCTGGTGATTATCACGGCAGGGGCGCGCCAGGAGAAGGGAGAAAC
CCGCCTGGACTTAGTCCAGCGGAATGTGGCCATCTTTAGATTGATGATTGCCAGTGTCGTCCAGTACAGCCCCCGCTGCA
AACTGATCGTGGTTTCCAACCCAGTGGATATCTTGACGTACGTAGCCTGGAAGTTGAGTGCGTTTCCCAAAAGCCGCGTT
ATCGGAAGTGGCTGTAATCTGGATACTGCTCGTTTCCGGTTTTTGATTGGACAAAAGCTTGGTATCCACTCCGAAAGCTG
TCACGGGTGGGTCCTTGGAGAACATGGAGACTCGAGTGTTCCCGTGTGGAGTGGAGTGAACATCGCTGGCGTCCTTCTAA
AAGATCTGAACGCAGCTATAGGTACTGGTAAGGACCCTGAGCAGTGGGAAAATGTCCACAAAGAAGTGGTTAACAGTGCC
TATGAGATTATTAAAATGAAAGGTTATACTTCATGGGCCATTGGCCTATCTGTAGCTGATTTAACAGAAAGTATCTTGAA
GAATCTCAGGAGAGTGCATCCAGTTTCCACCATAATTAAGGGTCTTTATGGAATAAATGAAGAAGTATTCCTCAGTGTTC
CTTGTGTCCTAGGAGAAAATGGTATAACAGACATTATAAAGATAAAGATGACCCCTGAAGAGGAGGCCCGCTTCAAAAAG
AGTGCAAAAACCCTTTGGGGAATTCAGAAGGAGCTCAAG

Alignment

ORF - retro_itri_535 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.67 %
• Parental protein coverage: 92.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKMASLKDQLIVNLLKEEQVPQNKITVVGVGAVGMACAISILMKDLADELALVDVMEDKLKGEMMDLQHG
          S.MA..K..L..NL..EE.V...K....G.G.VG.ACA.SIL.K.L.DELALVDV.E..LKGE..DLQ.G
Retrocopy SEMATVKGELFKNLAPEERVHHTKVSIIGSGSVGVACALSILLKGLSDELALVDVNEARLKGETLDLQQG

Parental  SLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPHCKLLIVSN
          S.F...P.IV...DY.VTA.S.LVIITAGARQ..GE.RL.LVQRNV.IF...I..VV.YSP.CKL..VSN
Retrocopy SAFAKLPSIVCSRDYLVTADSSLVIITAGARQEKGETRLDLVQRNVAIFRLMIASVVQYSPRCKLIVVSN

Parental  PVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGVNVAG
          PVDILTYVAWK.S.FPK.RVIGSGCNLD.ARFR.L.G..LG.H..SCHGWVLGEHGDSSVPVWSGVN.AG
Retrocopy PVDILTYVAWKLSAFPKSRVIGSGCNLDTARFRFLIGQKLGIHSESCHGWVLGEHGDSSVPVWSGVNIAG

Parental  VSLKNLHPDLGTDADKEHWKEVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPISTMIK
          V.LK.L....GT..D.E.W..VHK.VV.SAYE.IK.KGYTSWAIGLSVADL.ESI.KNLRRVHP.ST.IK
Retrocopy VLLKDLNAAIGTGKDPEQWENVHKEVVNSAYEIIKMKGYTSWAIGLSVADLTESILKNLRRVHPVSTIIK

Parental  GLYGIKDDVFLSVPCILGQNGISDVVKVNLTPEEEARLKKSADTLWGIQKELQ
          GLYGI...VFLSVPC.LG.NGI.D..K...TPEEEAR.KKSA.TLWGIQKEL.
Retrocopy GLYGINEEVFLSVPCVLGENGITDIIKIKMTPEEEARFKKSAKTLWGIQKELK

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_535 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_535 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 8 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009211	8 retrocopies	retro_cfam_1061, retro_cfam_1149, retro_cfam_1182, retro_cfam_1317, retro_cfam_1617, retro_cfam_1946, retro_cfam_2006, retro_cfam_309,
Dipodomys ordii	ENSDORG00000003524	2 retrocopies	retro_dord_439, retro_dord_449,
Felis catus	ENSFCAG00000015735	4 retrocopies	retro_fcat_102, retro_fcat_1839, retro_fcat_1919, retro_fcat_295,
Myotis lucifugus	ENSMLUG00000016343	4 retrocopies	retro_mluc_1716, retro_mluc_2031, retro_mluc_2440, retro_mluc_365,
Mustela putorius furo	ENSMPUG00000013730	5 retrocopies	retro_mputfur_1256, retro_mputfur_133, retro_mputfur_1446, retro_mputfur_1476, retro_mputfur_1565,
Ictidomys tridecemlineatus	ENSSTOG00000000014	3 retrocopies	retro_itri_1396, retro_itri_1526, retro_itri_535 ,
Ictidomys tridecemlineatus	ENSSTOG00000022058	2 retrocopies	retro_itri_501, retro_itri_648,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,