RetrogeneDB ID: retro_itri_282

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393282.1:1958383..1959278(+)
• Located in intron of: None

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_282
TGCGTGACATTCCCTCACCCAGACACCATGCCTGAACAGCAACTGCTACAGCCAACCGAGTGGAGCTACTGTGACTACTT
CTGGGCTGATAAGAAGGATCCCCAAGGCAATGGCACAGTGGCTGGGTTCGAACTGCTGATCCAAAAGCAACTGAAAGGCA
AACAAATGCAGAAAGAAACGTCTGAATTCGTCCGAGAGAGGATAAAGGTTGAAGAAAAACATGCAAAGAACTTGGCTAAG
CTCTCTCAGAACTCCTTGGCTGCACAGGAGGAAGGCTCCTTGGGAGAAGCCTGGGCCCAGGTGAAGAAGAATCTGGCAGA
TGAAGAAGAGGCTCATCTCAAGTTCTCCGCCAAGCTTCACAGCGAGGTCGAGAAGCCCCTAATGAACTTTTGTGAGAACT
TCAAGAAAGACATGAAAAAGTGTGACCACCATATCGCTGACCTCCGCTAGCAGCTCGCCAGCTGCTGCACGTCGGTGGAG
AAGGCCCGGAAAGCCCTCACAGAGCGGCAGAGAGACCTGGAGATGAAGACCCAGCAGCTGGAGATCAAGCTGAGCAACAA
GACAGAGGAGGACATCAAGAAGGCACGGAGAAAGTCCACACAGGCTGGCGATGACCTCATGTGCTGTGTGGGTCTCTACA
ACCAGGCGCAGTCCAAGTGGTTTGAAGAGATGGTGACCACCACTTTGGAGCTGGAGCGGCTGGAGGTGGAGAGGGTGGAG
ATGATCCGGCAACATCTGTGTCAGTACACACAGCTGCGGCATGAGACAGACATGTTCAACCAAAGCACAGTCGAGCCTGT
GGACCAACTGCTTCGAAAAGTGGACCCGGCCACCCCAGAGAGCTGTGGGTCAGAGAGCACAAAACGGCAACATTCGCCCT
GTGGACATGGAGATC

Alignment

ORF - retro_itri_282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.36 %
• Parental protein coverage: 71.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CVTFPHPDTMPEQQLLKPTEWSYCDYFWADKKDPQGNGTVAGFELLLQKQLKGKQMQKEMSEFVRERIKI
          CVTFPHPDTMPEQQLL.PTEWSYCDYFWADKKDPQGNGTVAGFELL.QKQLKGKQMQKE.SEFVRERIK.
Retrocopy CVTFPHPDTMPEQQLLQPTEWSYCDYFWADKKDPQGNGTVAGFELLIQKQLKGKQMQKETSEFVRERIKV

Parental  EEEYAKNLAKLSQNSLAAQEEGSLGEAWAQVKKSLADEAEVHLKFSAKLHSEVEKPLMNFRENFKKDMKK
          EE..AKNLAKLSQNSLAAQEEGSLGEAWAQVKK.LADE.E.HLKFSAKLHSEVEKPLMNF.ENFKKDMKK
Retrocopy EEKHAKNLAKLSQNSLAAQEEGSLGEAWAQVKKNLADEEEAHLKFSAKLHSEVEKPLMNFCENFKKDMKK

Parental  CDHHIADLRKQLASRYASVEKARKALTERQRDLEMKTQQLEIKLSNKTEEDIKKARRKSTQAGDDLMRCV
          CDHHIADLR.QLAS...SVEKARKALTERQRDLEMKTQQLEIKLSNKTEEDIKKARRKSTQAGDDLM.CV
Retrocopy CDHHIADLR*QLASCCTSVEKARKALTERQRDLEMKTQQLEIKLSNKTEEDIKKARRKSTQAGDDLMCCV

Parental  DLYNQAQSKWFEEMVTTTLELERLEVERVEMIRQHLCQYTQLRHETDMFNQSTVEPVDQLLRKVDPA-KD
          .LYNQAQSKWFEEMVTTTLELERLEVERVEMIRQHLCQYTQLRHETDMFNQSTVEPVDQLLRKVDPA...
Retrocopy GLYNQAQSKWFEEMVTTTLELERLEVERVEMIRQHLCQYTQLRHETDMFNQSTVEPVDQLLRKVDPA<HP

Parental  RELWVREHKT-GNIRPVDMEI
          RELWVREHKT.GNIRPVDMEI
Retrocopy RELWVREHKT<GNIRPVDMEI

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_282 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_282 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,