RetrogeneDB ID: retro_itri_135

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393683.1:177313..178114(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000022583
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: E2F6
• Ensembl ID: ENSSTOG00000003316
• Aliases: None
• Description: E2F transcription factor 6 [Source:HGNC Symbol;Acc:3120]

Sequence

>retro_itri_135
ACTGCCCCCATGGACGGCTCTGTGGAGAAGCTTTGCCGTCCCAACAACGTGGAGATGCTGCCACCGTCAAAAATACGGAG
GAATTTAGAAGGCAATGACCAAAATGCCTCCGGGAGTAGAGCTCTAAAAGGGAAGAAACCTCGTTTTAATGTGTCACTGG
TTTGTTTAACTAAAAGATTTACGGATCTCATCAAATCCGCTCCTGGGGGCATCCTGGACTTAAACAAGGCTGCGACAACC
CTGGGAGTACCGAAACGCAGACTCTATGACATTACGGGCGTCTTGAATGGAATTGACTTCGTGGAAAAGAAATCCAGGAA
CCACGTTCGATGGACAGGATCTGACCTTAGCCACTCCGAGGCACTAACCCAGAAACAGAAGCTGCAGGAGGAGCTTGCAA
ACTTAGCAGCAATGGAAGGTGCTTTGGATGAGTTGATTAAGGATTGTGCTCAGCAGTTGTTTGAGTTAACGGATGACAAA
ACAAATGAAAGTTTGGCCTATGTGACGTATCAGGATGTCCACAGCATTGAAGACTTTCATGAACAGATTGTCATTGCCGT
CAGAGCTCCAGAGGCAACCACGTTGGATGTTTTAGCTCCGGGAGAGGACAGTCTCACAGTTCACGTAAAGAGCACCAGAG
GACCCATCGACGTGTACTTGTGTGAAATGGAGCAGAACCACTCAAGTGGCAAGACATCTGACGGAGCAGAGACCTCTTCA
TCTGAAAGCCAACATCCAGAAGGCCATGAGGAAGGGGAAAACTCCCCTCAGCAAAGTGAAGATTTGCCTGAAGTAAACAA
C

Alignment

ORF - retro_itri_135 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.78 %
• Parental protein coverage: 94.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PAEETVRRRCRDPINVESLLPSKIRINLEDNVQYVSMRKALKVKRPRFDVSLVYLTRKFMDLVRSAPGGI
          P....V...CR.P.NVE.L.PSKIR.NLE.N.Q..S...ALK.K.PRF.VSLV.LT..F.DL..SAPGGI
Retrocopy PMDGSVEKLCR-PNNVEMLPPSKIRRNLEGNDQNASGSRALKGKKPRFNVSLVCLTKRFTDLIKSAPGGI

Parental  LDLNKVATKLGVRKRRVYDITNVLDGIDLVEKKSKNHIRWIGSDLNNLGAVPQQKKLQEELSDLSAMEDA
          LDLNK.AT.LGV.KRR.YDIT.VL.GID.VEKKS.NH.RW.GSDL....A..Q..KLQEEL..L.AME.A
Retrocopy LDLNKAATTLGVPKRRLYDITGVLNGIDFVEKKSRNHVRWTGSDLSHSEALTQKQKLQEELANLAAMEGA

Parental  LDELIKDCAQQLFELTDDKENERYPLTYVTYQDIHSIQAFHEQIVIAVKAPEETRLDVPAPKEDSITVHI
          LDELIKDCAQQLFELTDDK.NE...L.YVTYQD.HSI..FHEQIVIAV.APE.T.LDV.AP.EDS.TVH.
Retrocopy LDELIKDCAQQLFELTDDKTNE--SLAYVTYQDVHSIEDFHEQIVIAVRAPEATTLDVLAPGEDSLTVHV

Parental  RSTRGPIDVYLCEVEQNHSNGKTSDRVGTSSSKSKHPEHPEKGENL-QQGEDVLEVNN
          .STRGPIDVYLCE.EQNHS.GKTSD...TSSS.S.HPE..E.GEN..QQ.ED..EVNN
Retrocopy KSTRGPIDVYLCEMEQNHSSGKTSDGAETSSSESQHPEGHEEGENSPQQSEDLPEVNN

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_135 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_135 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000048286	1 retrocopy	retro_btau_1820,
Callithrix jacchus	ENSCJAG00000006910	1 retrocopy	retro_cjac_178,
Dasypus novemcinctus	ENSDNOG00000000258	1 retrocopy	retro_dnov_187,
Homo sapiens	ENSG00000169016	4 retrocopies	retro_hsap_2542, retro_hsap_2547, retro_hsap_2572, retro_hsap_4906,
Macropus eugenii	ENSMEUG00000007957	4 retrocopies	retro_meug_1169, retro_meug_860, retro_meug_882, retro_meug_893,
Myotis lucifugus	ENSMLUG00000003384	1 retrocopy	retro_mluc_864,
Macaca mulatta	ENSMMUG00000023225	1 retrocopy	retro_mmul_87,
Nomascus leucogenys	ENSNLEG00000014134	1 retrocopy	retro_nleu_2351,
Pongo abelii	ENSPPYG00000012646	1 retrocopy	retro_pabe_1,
Pan troglodytes	ENSPTRG00000011661	2 retrocopies	retro_ptro_1484, retro_ptro_3272,
Ictidomys tridecemlineatus	ENSSTOG00000003316	1 retrocopy	retro_itri_135 ,