RetrogeneDB ID: retro_itri_1440

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393487.1:2971980..2973437(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DET1
• Ensembl ID: ENSSTOG00000021107
• Aliases: None
• Description: de-etiolated homolog 1 (Arabidopsis) [Source:HGNC Symbol;Acc:25477]

Sequence

>retro_itri_1440
ATGGATCATCATGTTTCCACTATTAAACCTCGAAGAATCCAAAACCAAAATGTCATTCACCGATTGAAACGGCGGCGGAT
CAGTTCAGGCAAGGCAGGTCCTCATTGGCACCAGGTTGGAGTGTTCCACCAGAATGTCTTCCCTAACTTTACAGTTGCCA
ACGTTGAAAAACCTCCTTGTTTCTTGCGTACATTCTCACCTGATGGATGCTACTTTATTGCTTTTCCTTCTGACCAGACA
TCTCTTGAAATTTATGAGTACCAGGGCTGCCAAGCAGCAGAGGACCTATTGCAGGGATATGAGGGGGAGATCCTATCCAA
TGGCAATGACCAGAGGTCAGTCAACATCCGGGGCAGGCTTTTTGAACGATTTTTCGTCCTGCTGCACATTACAAATGTAG
CAGCCAATGGTGAGCACCTGAACCGGGAGAGTAGCCTCTTCACTGATAATTGCCGATGAGTGATCGTGGGCTCTGCTGCC
TACCTCCCGGATGAGCCTCACCCTCCTTTCTATGAAGTATATCGGAACAGTGAATCAGTAACCCCAAATCCACGGTCCCC
TCTAGAGGACTATTCCCTCCACATCATTGACCTTCACACTGGCCGCTTATGTGATACGCGCACATTCAAGTGTGATAAAG
TGGTCTGTCACACAATCAAGGGCTGTACTTGTATAAAAACATCCTGGCCATCTTGTCTGTGCAGCAGCAGACCATCCATG
TCTTCCAGGTGACTCCTGAAGGCACATTCATTGATGTGCGGACCATTGGCCGCTTCTGCTATGAGGATGACCTGTTTACT
GTGTCGGCTGTTTTCCCTGAAGTACAGCAGGACAGTCAGACAGGCATGGCCAATCCCTTTAGGGATCCTTTCATCAACTC
CCTAAAACACCGGTTGCTGGTATACCTGTGGCGCCGGGCAGAACAGGATGGTAGTGCAATGGCCAAGAGGCGCTTCTTCC
AGTATTTTGACCAGCTGCGGCAGCTGCGTATGTGGAAAATGCAGCTTTTGGATGAAAACCATCTGTTTATCAAGTATACC
AGTGAGGATGTAGTGACACTGCGAGTCACTGATCCATCTCAGGCATCTTTGTTTGTAGTGTACAATATGGTGACAACTGA
AGTGATTGCTGTGTTTGAGAATACATCGGATGAACTTTTGGAACTCTTTGAGAACTTCTGTGATCTCTTCCATAATGCTA
CCTTGCACAGTGAAGTCCAATTTCCCTACTCAGCCTCCAGCAACAATTTTGCAAGGCAGATCCAGCGCCGGTTCAAAGAC
ACGATTATAAATGCCAAGTACGGAGGCCACATAGAGGCTGTGCGCCGGCAGCTGGGTCAGCTCCCCATCAGTGCACAGTC
CTACAGTGGCAGCCCCTACCTGGATTTGTCTCTCTTCAGCTACGATGACAAATGGGTGTCAGTCATGGAGCGACCCAAGA
CTTGTGGAGATCACCCC

Alignment

ORF - retro_itri_1440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.3 %
• Parental protein coverage: 88.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDHHVSTIKPRRIQNQNVIHRLERRRISSGKAGTHWHQVRVFHQNVFPNFTVVNVEKPPCFLRKFSPDGR
          MDHHVSTIKPRRIQNQNVIHRL.RRRISSGKAG.HWHQV.VFHQNVFPNFTV.NVEKPPCFLR.FSPDG.
Retrocopy MDHHVSTIKPRRIQNQNVIHRLKRRRISSGKAGPHWHQVGVFHQNVFPNFTVANVEKPPCFLRTFSPDGC

Parental  YFIAFSSDQTSLEIYEYQGCQAAEDLLQGYEGEILSNGNDQRSVNIRGRLFERFFVLLHITNVAANGEHL
          YFIAF.SDQTSLEIYEYQGCQAAEDLLQGYEGEILSNGNDQRSVNIRGRLFERFFVLLHITNVAANGEHL
Retrocopy YFIAFPSDQTSLEIYEYQGCQAAEDLLQGYEGEILSNGNDQRSVNIRGRLFERFFVLLHITNVAANGEHL

Parental  NRECSLFTDDCRCVIVGSAAYLPDEPHPPFYEVYRNSESVTPNPRSPLEDYSLHIIDLHTGRLCDTRTFK
          NRE.SLFTD.CR.VIVGSAAYLPDEPHPPFYEVYRNSESVTPNPRSPLEDYSLHIIDLHTGRLCDTRTFK
Retrocopy NRESSLFTDNCR*VIVGSAAYLPDEPHPPFYEVYRNSESVTPNPRSPLEDYSLHIIDLHTGRLCDTRTFK

Parental  CDKVV-LSHNQGLYLYKNILAILSVQQQTIHVFQVTPEGTFIDVRTIGRFCYEDDLLTVSAVFPEVQRDS
          CDKVV.LSHNQGLYLYKNILAILSVQQQTIHVFQVTPEGTFIDVRTIGRFCYEDDL.TVSAVFPEVQ.DS
Retrocopy CDKVV<LSHNQGLYLYKNILAILSVQQQTIHVFQVTPEGTFIDVRTIGRFCYEDDLFTVSAVFPEVQQDS

Parental  QTGMANPFRDPFINSLKHRLLVYLWRRAEQDGSAMAKRRFFQYFDQLRQLRMWKMQLLDENHLFIKYTSE
          QTGMANPFRDPFINSLKHRLLVYLWRRAEQDGSAMAKRRFFQYFDQLRQLRMWKMQLLDENHLFIKYTSE
Retrocopy QTGMANPFRDPFINSLKHRLLVYLWRRAEQDGSAMAKRRFFQYFDQLRQLRMWKMQLLDENHLFIKYTSE

Parental  DVVTLRVTDPSQASFFVVYNMVTTEVIAVFENTSDELLELFENFCDLFRNATLHSEVQFPCSASSNNFAR
          DVVTLRVTDPSQAS.FVVYNMVTTEVIAVFENTSDELLELFENFCDLF.NATLHSEVQFP.SASSNNFAR
Retrocopy DVVTLRVTDPSQASLFVVYNMVTTEVIAVFENTSDELLELFENFCDLFHNATLHSEVQFPYSASSNNFAR

Parental  QIQRRFKDTIINAKYGGHTEAVRRLLGQLPISAQSYSGSPYLDLSLFSYDDKWVSVMERPKTCGDHP
          QIQRRFKDTIINAKYGGH.EAVRR.LGQLPISAQSYSGSPYLDLSLFSYDDKWVSVMERPKTCGDHP
Retrocopy QIQRRFKDTIINAKYGGHIEAVRRQLGQLPISAQSYSGSPYLDLSLFSYDDKWVSVMERPKTCGDHP

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_1440 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1440 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
Macropus eugenii	ENSMEUG00000016149	1 retrocopy	retro_meug_1331,
Ictidomys tridecemlineatus	ENSSTOG00000021107	1 retrocopy	retro_itri_1440 ,