RetrogeneDB ID: retro_itri_133

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393350.1:7964225..7964705(+)
• Located in intron of: ENSSTOG00000013906

Retrocopy information

• Ensembl ID: ENSSTOG00000025417
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SFT2D2
• Ensembl ID: ENSSTOG00000022560
• Aliases: None
• Description: SFT2 domain containing 2 [Source:HGNC Symbol;Acc:25140]

Sequence

>retro_itri_133
ATGGAGAAGTTGCGGTGCGTCCTGAGTGGCCAGGACGACGAGGAGCAGGGCCTGACCGCGCAGGTCCTGGATGCCTCATC
TCTTAGTTTCAACACCAGATTGAAATGGTTTATCATATACTTTGTGGCTGGCATTTTCTTTTCTATCCTTGGAACTGCAT
TGCTGTGGCTTCCTGGCGGCATAAAGCTTTTTGCAGTGTTTTATACCCTTGGGAATCTTGCTACATTAGCCAGTACGTGC
TTTTTAATAGGACCCGTGAAGCAGCTAAAGAAAATGTTTGAAAAAACTAGAGTACTTGCAACAGTCATTATGCTTCTCTG
CCTCATATTCACCCTGTGTGCCGCTCTTTGGTGGCATAAGAAGGGACTGGCCTTACTATTCTGCATATTGCAGTTCTTAT
CAATGACCTGGTATAGTCTGTCGTACATCCCATATGCAAGAGATGCGGTACTTAAATGCTGCTCTTCTCTTCTAAGTTGA

Alignment

ORF - retro_itri_133 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVVEASSLSWGTRVKGFIACFAVGILCSLLGTLLLWVPKKGLTLFAVFYTFGNIASIGSTIFLMGPLKQL
          QV..ASSLS..TR.K.FI..F..GI..S.LGT.LLW.P..G..LFAVFYT.GN.A...ST.FL.GP.KQL
Retrocopy QVLDASSLSFNTRLKWFIIYFVAGIFFSILGTALLWLPG-GIKLFAVFYTLGNLATLASTCFLIGPVKQL

Parental  KRMFEPTRLIATILVLLCFALTLCSAFWWHNKGLALIFCILQSLSLTWYLCSFLP--RDAVKKCFAVCLA
          K.MFE.TR..AT...LLC...TLC.A.WWH.KGLAL.FCILQ.LS.TWY..S..P..RDAV.KC....L.
Retrocopy KKMFEKTRVLATVIMLLCLIFTLCAALWWHKKGLALLFCILQFLSMTWYSLSYIPYARDAVLKCCSSLLS

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_133 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_133 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010720	1 retrocopy	retro_acar_131,
Callithrix jacchus	ENSCJAG00000016838	1 retrocopy	retro_cjac_2771,
Monodelphis domestica	ENSMODG00000002896	1 retrocopy	retro_mdom_607,
Mustela putorius furo	ENSMPUG00000000531	1 retrocopy	retro_mputfur_1560,
Nomascus leucogenys	ENSNLEG00000014912	1 retrocopy	retro_nleu_2370,
Rattus norvegicus	ENSRNOG00000003038	1 retrocopy	retro_rnor_1135,
Sarcophilus harrisii	ENSSHAG00000018938	1 retrocopy	retro_shar_212,
Ictidomys tridecemlineatus	ENSSTOG00000022560	1 retrocopy	retro_itri_133 ,