RetrogeneDB ID: retro_itri_1209

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393401.1:1391640..1392390(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRIM44
• Ensembl ID: ENSSTOG00000023760
• Aliases: None
• Description: tripartite motif containing 44 [Source:HGNC Symbol;Acc:19016]

Sequence

>retro_itri_1209
GGGGAGAGGCCCGGGAAGGAAGAGATCACGGTCAAGGTGGAGCCGCCGCGGCAGGAGCTAGAAAGCGCCTTGGAGGACAG
TGACTCGGAAGGAGGGAGCGAGACCGGTGAGGAGAGTGAAGAGGAGGACAGTGAGCCAGAAAGCGAGATGATGGAAGAAG
ACATCCAAGGAAGGTGCATGTCGGAAAGAGAAACTAAGGCAGAAAGCAAATTCGACCCAAAAAGAGCACTGGAAGAAAAG
AGAACATCCAAGAGGAAGTATGCAGACCCAGGGCTTGATTTGAGCCCCTACTCCCAGAAAGACAGGCCCATCATCTGTGT
CCTTGGGACTCAGCAGGGTCACCAGCTTTACACCTTAGATGAAGCCTTTGAAGAACTAATAAGCAAAGACTCCACTAGAG
TGAAGGCAGCCATTATAGAGTTGGTGGAAAAGTTAAAGCTCAAGAGTTCAGATCCTAAAGTAACTCAGAAAGAGATAAAG
GAGTTCATACAAAAAGAATTTAAGAAAGTTCAGCAAGTGCTGGCTGATGAGGAGCATAAAGCTGTTCATCTAGTGGATAT
CCAGGAAGAAATGGACAGAGATCATCTAACTGAGATACTGGCAGACCTTCAGTCCCGAATGGATAAGCCGAGGACTCAGA
TGCCCCAGGCCAAGGAACAACTGGGTACCTCTAACAAATCAGCTAAGCCAAGGGCAGGGTGTGCTTAGGAAGGGGACCCA
GTAGTGCCAGGGAATAAGAGAGCACATGAA

Alignment

ORF - retro_itri_1209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.91 %
• Parental protein coverage: 71.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GEESESEEDSESEEESETEEESE-DESDEESDEDSEEEMEDEQ---ESEAEEDNQEGESEAEGETEAESE
          GE....EE.....E....E.ES....SD.E......EE.E.E....ESE..E....G....E.ET.AES.
Retrocopy GERPGKEEITVKVEPPRQELESALEDSDSEGGSETGEESEEEDSEPESEMMEEDIQGRCMSERETKAESK

Parental  FDPEIEMEAERVAKRKCPDHGLDLSTYCQEDRQLICVLCPVIGAHQGHQLSTLDEAFEELRSKDSGGLKA
          FDP....E..R..KRK..D.GLDLS.Y.Q.DR..ICVL....G..QGHQL.TLDEAFEEL.SKDS...KA
Retrocopy FDPKRALEEKRTSKRKYADPGLDLSPYSQKDRPIICVL----GTQQGHQLYTLDEAFEELISKDSTRVKA

Parental  AMIELVERLKFKSSDPKVTRDQMKVFIQQEFKKVQKVIADEEQKALHLVDIQEAMATAHVTEILADIQSH
          A.IELVE.LK.KSSDPKVT....K.FIQ.EFKKVQ.V.ADEE.KA.HLVDIQE.M...H.TEILAD.QS.
Retrocopy AIIELVEKLKLKSSDPKVTQKEIKEFIQKEFKKVQQVLADEEHKAVHLVDIQEEMDRDHLTEILADLQSR

Parental  MDRLMTQMAQAKEQLDTSNESAEPKA----EGDEEGPSGASEEE
          MD...TQM.QAKEQL.TSN.SA.P.A....EGD...P......E
Retrocopy MDKPRTQMPQAKEQLGTSNKSAKPRAGCA*EGDPVVPGNKRAHE

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_1209 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1209 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011263	1 retrocopy	retro_cpor_1385,
Ictidomys tridecemlineatus	ENSSTOG00000023760	1 retrocopy	retro_itri_1209 ,