RetrogeneDB ID: retro_itri_1111

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393378.1:3353912..3354346(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000001426
• Aliases: None
• Description: None

Sequence

>retro_itri_1111
AGTACCAGAAAGCATTTGCAAACTATGATAGAATCAGTAATAATAGCAATTTTGAGTAACAATATTGAAGAAAAAGAACA
AATCGAATGTCATCTCAACTACCTGAATATAAGATTGCTACAATTGTGTGAAACCATGAAAATCCCTAACCCAAAAGCTG
AAATATTTTATTAATGTGCCAAATCTACTGAAAATGGAGAAAGCACAAGACAAAACTATTGAAGAAAGTCTGGCATTATT
GTAGAAAGAAATAGATAAAATTGTAGAGACCACAGAATCAATGATTGGAGATATTCAGAGACTAAAAAGTAGAATTCAAA
TTGTGACACATGAGATAGAAGGAAGAGGAGGTAAAACAGATGTTTCAAATAGCTTATAGTGGGGTATTCTCTTTTCCAGG
ACTTTCTCAGAACAGTCTCAAAGCACCCACACTA

Alignment

ORF - retro_itri_1111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.32 %
• Parental protein coverage: 53.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  STREHLQTMIESVIIAILSNKIKEKEQIQCHLNYLKIRLLQLCETMKVP-PRKLKYLTNVSNLLKMEKAQ
          STR.HLQTMIESVIIAILSN.I.EKEQI.CHLNYL.IRLLQLCETMK.P...KLKY..NV.NLLKMEKAQ
Retrocopy STRKHLQTMIESVIIAILSNNIEEKEQIECHLNYLNIRLLQLCETMKIP>TQKLKYFINVPNLLKMEKAQ

Parental  ETANEEGLALLQEEIDKMVETTESMTENIHRLKNKIQIVAHEVE-EEEEKVKQMLQMDSSGVLSLPELSQ
          ....EE.LALL..EIDK.VETTESM...I.RLK..IQIV.HE.E.EEE..VKQM.Q...SGV.S.P.LSQ
Retrocopy DKTIEESLALL*KEIDKIVETTESMIGDIQRLKSRIQIVTHEIE>EEE--VKQMFQIAYSGVFSFPGLSQ

Parental  NSLKAPTL
          NSLKAPTL
Retrocopy NSLKAPTL

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_1111 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1111 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000345	1 retrocopy	retro_chof_1088,
Oryctolagus cuniculus	ENSOCUG00000006103	1 retrocopy	retro_ocun_32,
Ictidomys tridecemlineatus	ENSSTOG00000001426	1 retrocopy	retro_itri_1111 ,
Tupaia belangeri	ENSTBEG00000004322	1 retrocopy	retro_tbel_1115,