RetrogeneDB ID: retro_itri_466

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393293.1:2183913..2184807(-)
• Located in intron of: ENSSTOG00000020865

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAS7
• Ensembl ID: ENSSTOG00000022185
• Aliases: None
• Description: growth arrest-specific 7 [Source:HGNC Symbol;Acc:4169]

Sequence

>retro_itri_466
AATTGCGTGACATTCCCTCACCCAGACACCATGCCTGAACAGCAACTGTTAAAGCCAACCGAGTGGAGCTACTGTGACTA
CTTCTGGGCGGATAAGAAGGATCCCCAAGGCAATGGCACGGTGGCTGGGTTCAAACTGCTGATCCAAAAGCAACTGAAGG
GCAAACAAATGCAGAAAGAAATGTCTGAATTCTTCTGAGAGAGGATAAAGATTGAAGAAGAATATGCAAAGAACCTGGCT
AAGCTCTCTCAGAACTCCTTGGCTGCATAGGAGGAAGGCTCCTTGGGAGAAGCCTGGGCCCAGGTGAAGAAGAGTCTGGC
AGATGAAGCAGAGGTTCATCTCAAGTTCTCCGCTAAGCTTCACAGCGAGGTAGAGAAGCCCCTAATGAACTTTCGTGAGA
ACTTCAAGAAAGACATGAAAAAGTGTGACCACCATATCGATGACCTCCGCAAGCAGCTCGCCAGCCGCTAAGCATTGGTG
GAGAAGGCCCGGAAAGCCCTCACAGAGCGGCAGAGAGACCTGGAGATGAAGACCCAGCAGCTGGAGATCAAGCTGAGCAA
TAAGACAGAGGAGGACATCAAGAAGGCATGGAGAAAGTCCACACAGGCTGGTGATGACCTCGTGCGTTGTGTGGACCTCT
ACAACCAGGCGCAGTCCAAGTGGTTTGAAGAGATGGTGACCACCACTTTGGAGCTGGAGCGGCTGGAGGTGGAGAGGGTA
GAGATGATCCGGCAACATCTGAGTCAGTACACACAGCTGCGGCATGAGACAGATATGTTCAACCAAAGCACAGTTGAGCC
TGTGGACCAACTGCTTCGAAAAGTGGACCCAGCCAAAGACAGAGAGCTGTGGGTCAGAGAGCACAAAACGGGCAACATTC
GCCCTGTGGACATG

Alignment

ORF - retro_itri_466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.31 %
• Parental protein coverage: 70.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NCVTFPHPDTMPEQQLLKPTEWSYCDYFWADKKDPQGNGTVAGFELLLQKQLKGKQMQKEMSEFVRERIK
          NCVTFPHPDTMPEQQLLKPTEWSYCDYFWADKKDPQGNGTVAGF.LL.QKQLKGKQMQKEMSEF..ERIK
Retrocopy NCVTFPHPDTMPEQQLLKPTEWSYCDYFWADKKDPQGNGTVAGFKLLIQKQLKGKQMQKEMSEFF*ERIK

Parental  IEEEYAKNLAKLSQNSLAAQEEGSLGEAWAQVKKSLADEAEVHLKFSAKLHSEVEKPLMNFRENFKKDMK
          IEEEYAKNLAKLSQNSLAA.EEGSLGEAWAQVKKSLADEAEVHLKFSAKLHSEVEKPLMNFRENFKKDMK
Retrocopy IEEEYAKNLAKLSQNSLAA*EEGSLGEAWAQVKKSLADEAEVHLKFSAKLHSEVEKPLMNFRENFKKDMK

Parental  KCDHHIADLRKQLASRYASVEKARKALTERQRDLEMKTQQLEIKLSNKTEEDIKKARRKSTQAGDDLMRC
          KCDHHI.DLRKQLASR.A.VEKARKALTERQRDLEMKTQQLEIKLSNKTEEDIKKA.RKSTQAGDDL.RC
Retrocopy KCDHHIDDLRKQLASR*ALVEKARKALTERQRDLEMKTQQLEIKLSNKTEEDIKKAWRKSTQAGDDLVRC

Parental  VDLYNQAQSKWFEEMVTTTLELERLEVERVEMIRQHLCQYTQLRHETDMFNQSTVEPVDQLLRKVDPAKD
          VDLYNQAQSKWFEEMVTTTLELERLEVERVEMIRQHL.QYTQLRHETDMFNQSTVEPVDQLLRKVDPAKD
Retrocopy VDLYNQAQSKWFEEMVTTTLELERLEVERVEMIRQHLSQYTQLRHETDMFNQSTVEPVDQLLRKVDPAKD

Parental  RELWVREHKTGNIRPVDM
          RELWVREHKTGNIRPVDM
Retrocopy RELWVREHKTGNIRPVDM

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_466 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_466 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 1 parental gene, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000022185	12 retrocopies	retro_itri_1040, retro_itri_1162, retro_itri_1203, retro_itri_1216, retro_itri_1416, retro_itri_1672, retro_itri_1733, retro_itri_282, retro_itri_294, retro_itri_372, retro_itri_466 , retro_itri_762,