RetrogeneDB ID: retro_itri_1040

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393361.1:5183713..5184595(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000020400
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1040
TGTGTGACATTCCCTCACCCAGACACCATGCCTGAACAGCAACTGCTAAAGCCAACCGAGTGGAGCTACTGTGACTACTT
CTGGGCTGATAAGAAGGATCCCCAAGGCAATGGCACAGTGGCTGGGTTCGAACGGCTGCTCCAAAAGCAAATGAAGGGCA
AACAAATGCAGAAAGAAATGTCTGAATTCGTCCGAGAGAGGATAAAGGTTAAAGAAGAATATGCAAAGAACTTGGCTAAG
CTCTCTCAGAACTCCTTGGCTGCACAGGAGGAAGGCTCCTTGGGAGAAGCCTGGGCCCAGGTGAAGAAGAATCTGGCAGA
TGAAGCAGAGGTTCATCTCAAGTTCTCCGCCAAGCTTCACAGTGAGATAGAGAAGCCCCTAATGAACTTTCGTGAGAACT
TCAAGAAAGACTTGAAAAAGTGTGACCACCATATTGCTGACCTCCGCAAGCAGCTCGCCAGCCGCTATGTGTCGGTGGAG
AAGGCCGGGAAAGCCCTCACAGAGCGGCAGAGGAAGACCCAGCAGCTGGAGATCAAGCTGAGCAACAAGACAGAGGAGGA
CATCAAGAAGGCACGGAGAAAGTCCACACAGGCTGGCGATGACCTCATGTGCTGTGTGGACCTCTACAAGCAGGCCCAGT
CCAGGTGGTTTGAAGAGATGGTGACCACCACTTTGGAGCTGGAGCGGCTGGAGGTGGAGAGGGTGGAGATGATCCGGCAA
GATCTGTGTCAGTACACACAGCTGCGGCATGAGACAGATATGTTCAACCAAAGCACAGTCGAGCCTGTGGACCAACTGCT
TCGAAAAGTGGACCCCCCCGGCCAAAGACAGAGAGCTGTGGGTCAGAGAGCACAAAACGGGCAACATTGCCCCGTGGACA
TG

Alignment

ORF - retro_itri_1040 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.26 %
• Parental protein coverage: 70.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CVTFPHPDTMPEQQLLKPTEWSYCDYFWADKKDPQGNGTVAGFELLLQKQLKGKQMQKEMSEFVRERIKI
          CVTFPHPDTMPEQQLLKPTEWSYCDYFWADKKDPQGNGTVAGFE.LLQKQ.KGKQMQKEMSEFVRERIK.
Retrocopy CVTFPHPDTMPEQQLLKPTEWSYCDYFWADKKDPQGNGTVAGFERLLQKQMKGKQMQKEMSEFVRERIKV

Parental  EEEYAKNLAKLSQNSLAAQEEGSLGEAWAQVKKSLADEAEVHLKFSAKLHSEVEKPLMNFRENFKKDMKK
          .EEYAKNLAKLSQNSLAAQEEGSLGEAWAQVKK.LADEAEVHLKFSAKLHSE.EKPLMNFRENFKKD.KK
Retrocopy KEEYAKNLAKLSQNSLAAQEEGSLGEAWAQVKKNLADEAEVHLKFSAKLHSEIEKPLMNFRENFKKDLKK

Parental  CDHHIADLRKQLASRYASVEKARKALTERQRDLEMKTQQLEIKLSNKTEEDIKKARRKSTQAGDDLMRCV
          CDHHIADLRKQLASRY.SVEKA.KALTERQR....KTQQLEIKLSNKTEEDIKKARRKSTQAGDDLM.CV
Retrocopy CDHHIADLRKQLASRYVSVEKAGKALTERQR----KTQQLEIKLSNKTEEDIKKARRKSTQAGDDLMCCV

Parental  DLYNQAQSKWFEEMVTTTLELERLEVERVEMIRQHLCQYTQLRHETDMFNQSTVEPVDQLLRKVDPAKDR
          DLY.QAQS.WFEEMVTTTLELERLEVERVEMIRQ.LCQYTQLRHETDMFNQSTVEPVDQLLRKVDP...R
Retrocopy DLYKQAQSRWFEEMVTTTLELERLEVERVEMIRQDLCQYTQLRHETDMFNQSTVEPVDQLLRKVDPPGQR

Parental  ELWVREH-KTGNIRPVDM
          ...V......G...PVDM
Retrocopy QRAVGQRAQNGQHCPVDM

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_1040 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1040 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,