RetrogeneDB ID: retro_itri_1733

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393687.1:314224..315103(+)
• 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_1733
TGTGTGACATTCCCTCACCCAGCACAATGCAACTGCTAAAGCCAACAGAGTGGAGCACTGTGACTACTTCTGAGCTGATA
AGAAAGATCCCCAAGGCAATGGCACCATGGCTGGGTTCAAACTGCTGTTCCAAAAGCAACTGAAAGGCAAACAAATGCAG
AAAGAAATGTCTGAATTCCTCTGAGAGAGGATAAAGATTGAAGAAGAATATGCAAAGAACTTGGCTAAGCTCTCTCAGAA
CTCCTTGGCTGCACAGGAGGAAGGCTTCCTGGGAGAAGCGTGGTCCCTGGTGAAGAGCCCAGCAGATGAAGCAAGTTCTC
TGCCAAATTCTCCACCAAGCTTCACAGCGAGGTAGAGAAGCCCCTAATGAACTTTCCTGAGAATTTCAAGAAAGACGTGA
AAAAGTGTGACCACCATATCGTTGACCTCTGCTAGCAGCTCGCTAACTGCTATGCATTAGTGGAGAAGGCCTGGAAAGCC
CTCACAGAGTGGCAGAGAGACCTGGAGATGAAGACCCAGCAGCTGGAGATCAAGCTGAGCAAAAAGACAAAGGAGGACAT
CAAGAAGGAACAGAGAAAGTCCACACAGGCTGGTGATAATCTCATGCACTGTGTGGACCTCTACAACCAGGCCCAGTCCA
AGTGGTTTGAAGAGATGGTGACCACCACTTTGGAGCTGGGGCAGCTGGAGGTGGAGAGGGTGGAAATGATCCAACAATAT
CTGTGCCAGTACACACAGCTGCAGCATGAGACAGACATGTTCAACCAAAGCACAGTCGAGCCTGTGGACCAACTGCTTCG
AAAAGTGGACCCAGCCAAAGACAGACAGCTATGGGTCAGAGAGCACAAAATAGGCAACATTCGCCCTGTGGACATGGAC

Alignment

ORF - retro_itri_1733 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.05 %
• Parental protein coverage: 70.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CVTFPH-PDTMPEQQLLKPTEWS-YCDYFWADKKDPQGNGTVAGFELLLQKQLKGKQMQKEMSEFVRERI
          CVTFPH.P.TM...QLLKPTEWS..CDYF.ADKKDPQGNGT.AGF.LL.QKQLKGKQMQKEMSEF..ERI
Retrocopy CVTFPH<PSTM---QLLKPTEWS<HCDYF*ADKKDPQGNGTMAGFKLLFQKQLKGKQMQKEMSEFL*ERI

Parental  KIEEEYAKNLAKLSQNSLAAQEEGSLGEAWAQVKKSLADEA-EVHLKFSAKLHSEVEKPLMNFRENFKKD
          KIEEEYAKNLAKLSQNSLAAQEEG.LGEAW..VK.S.ADEA.....KFS.KLHSEVEKPLMNF.ENFKKD
Retrocopy KIEEEYAKNLAKLSQNSLAAQEEGFLGEAWSLVK-SPADEA<KFSAKFSTKLHSEVEKPLMNFPENFKKD

Parental  MKKCDHHIADLRKQLASRYASVEKARKALTERQRDLEMKTQQLEIKLSNKTEEDIKKARRKSTQAGDDLM
          .KKCDHHI.DL..QLA..YA.VEKA.KALTE.QRDLEMKTQQLEIKLS.KT.EDIKK..RKSTQAGD.LM
Retrocopy VKKCDHHIVDLC*QLANCYALVEKAWKALTEWQRDLEMKTQQLEIKLSKKTKEDIKKEQRKSTQAGDNLM

Parental  RCVDLYNQAQSKWFEEMVTTTLELERLEVERVEMIRQHLCQYTQLRHETDMFNQSTVEPVDQLLRKVDPA
          .CVDLYNQAQSKWFEEMVTTTLEL..LEVERVEMI.Q.LCQYTQL.HETDMFNQSTVEPVDQLLRKVDPA
Retrocopy HCVDLYNQAQSKWFEEMVTTTLELGQLEVERVEMIQQYLCQYTQLQHETDMFNQSTVEPVDQLLRKVDPA

Parental  KDRELWVREHKTGNIRPVDME
          KDR.LWVREHK.GNIRPVDM.
Retrocopy KDRQLWVREHKIGNIRPVDMD

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_1733 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1733 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,