RetrogeneDB ID: retro_itri_1101

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393376.1:6760255..6760862(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDE1
• Ensembl ID: ENSSTOG00000019896
• Aliases: None
• Description: nudE nuclear distribution E homolog 1 (A. nidulans) [Source:HGNC Symbol;Acc:17619]

Sequence

>retro_itri_1101
ACCGAATTCATTAAAGATCAGCTGCAGAAATACATCGGGGAGCTGGAGCAAGCAAAAGATGATGTGGAAAGAGCAAAATG
AGCCAGGATCTTGTCTCTGGAAGACGTTGAGCAGCGCTTGAATGGAGCCATTGAAAGAAATACCTTTCTGGAAAGTGAAC
TTGATGAAAAGGAGAAACTCCTAGAATCCATTCAGCAACTAAAGGAGGAAGCTAGAGATTTGCAGTGGGAATTGCAGCAG
AAGCAGGAGAAGCCCAGGACGCCCATGACCACTCCATAGAACCTGAAAGGACAGGCACAGCTGTGCAAGCCACAGGCTCT
GTGCCATCCACTCCCTTATTGCATCTAGGACCCAGCTGTGGCTGGTATACACCAGGGACATTCAAATATGGTCTGAATAG
CTCCAACAGTGGGACCCCCTGAGGGCTGCAGCCTGGATTTCAGCTCTCAACATTGTCGGGGACTTGCTTCAGAAAGTAGC
TGCACTGGAATCCAAACTGACATCCTGACAGAACTTCATGTATGATCAGTCCCCAAACCTGACAGGCAACCCTGTCTCAG
GGCAGGGGAGCAAGGACAGAGACAGCACAGACCCACAAGCAACATCC

Alignment

ORF - retro_itri_1101 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.46 %
• Parental protein coverage: 59.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TRAIRDQLQKYIRELEQANDDLERAKRATIMSLEDFEQRLNQAIERNAFLESELDEKENLLESVQRLKDE
          T..I.DQLQKYI.ELEQA.DD.ERAK.A.I.SLED.EQRLN.AIERN.FLESELDEKE.LLES.Q.LK.E
Retrocopy TEFIKDQLQKYIGELEQAKDDVERAK*ARILSLEDVEQRLNGAIERNTFLESELDEKEKLLESIQQLKEE

Parental  ARDLRQELAVQQKQEKPRTPMPS-SAEAERTDTAVQATGSVPSTPVAHRGPSSSLNTPGTFKRGLDHSNS
          ARDL..EL..QQKQEKPRTPM...S.E.ERT.TAVQATGSVPSTP..H.GPS....TPGTFK.GL..SNS
Retrocopy ARDLQWEL--QQKQEKPRTPMTT<SIEPERTGTAVQATGSVPSTPLLHLGPSCGWYTPGTFKYGLNSSNS

Parental  GT-PLTPAARISALNIVGDLLRKVGALESKLASCRNFVYDQSPNRTGGPASGRGSKNRDGGDRRTSS
          GT.PL..AA.ISALNIVGDLL.KV.ALESKL.S..NF.YDQSPN.TG.P.SG.GSK.RD..D....S
Retrocopy GT<PLRAAAWISALNIVGDLLQKVAALESKLTS*QNFMYDQSPNLTGNPVSGQGSKDRDSTDPQATS

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_1101 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1101 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009557	1 retrocopy	retro_amel_104,
Canis familiaris	ENSCAFG00000018722	1 retrocopy	retro_cfam_1579,
Choloepus hoffmanni	ENSCHOG00000006004	1 retrocopy	retro_chof_1270,
Cavia porcellus	ENSCPOG00000019614	2 retrocopies	retro_cpor_875, retro_cpor_876,
Ictidomys tridecemlineatus	ENSSTOG00000019896	1 retrocopy	retro_itri_1101 ,
Ictidomys tridecemlineatus	ENSSTOG00000027930	1 retrocopy	retro_itri_620,
Tupaia belangeri	ENSTBEG00000005260	1 retrocopy	retro_tbel_1468,