RetrogeneDB ID: retro_itri_1904

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH398903.1:731..1969(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DLG5
• Ensembl ID: ENSSTOG00000022087
• Aliases: None
• Description: discs, large homolog 5 (Drosophila) [Source:HGNC Symbol;Acc:2904]

Sequence

>retro_itri_1904
AAGAAGTCCCAACTGGACTTTGGGGTGCATTTGTGTGGTGGGAACCTGCACAGGGTGTTTGTGGCCGAAGTAGAGGATGA
CAGTCCTGCCAGGGGTCCCGATGGCCTGGTGCCAGGAGACCTAATCCTCGAGTATGGCAACCTGGATGTGCACAATAAGA
TGGTGGACGAGGTCTACGTGGAGATGCTGAAGCCCAAAGACAGTATCCGCCTGAAGGTGTAGTACCGCCCAGAGGAGTTC
ACCAGGATCAAGGGCCTGCCTGGTGACAGCTTCTACATCAGGGCCCTGTATGACCGGCTGGCCGAGGTGGAGCATGAGCT
GAGCTTTAGGAAGGAGGACATTCTCTAGTGGATGACACCTTGCCCCAGGGCACATTTGGGTCCTGGATGGCGTGGCATCT
GGATGAGAACGCCCAGAATATCCAGCGTTGGCATATTCCCAGCAAATGTGTGATGGATCAAGAATTCTCCATGAGGCTCA
GCATGTCCGAGGTCAAAGACAGTAGTGCCACCAAGACGCTGTCAGCAGCTGCTTGCTGGTCCTTCTTTGGAAGGAAGCAC
AAGCACAAATGCAATGGGTCCAAAGACAGGAAAGACCTCCTGGCCTTGGACACCTTCTCCAACGACTCCCTCTAGCTCTT
TGAAGATTCAGTGAGTCTGGCCTATCAGCAGGTCCAGAAGGTGGACTGCATCTCTCTGAGGCCTGTCCTGATTCTGGGGC
CTCTGCTGGATATGGTGAAGGAAATGCTGATAAATGAGGTCCCTGGCAAGTTCTGCAGATGCCCGTTGAAAGTGATGAAG
GCCTCCCAGCAGGCCATTGAGCGGGGCATTAAAGACTGCCTGTTTGTCGACTACAAACGGAGGAATGGCCATTTTGATGT
GACCATGGTGGCTTCAATAAAGGAGATCACAGAAAAGAACCGGCACTGCCTCCTGGACGTCGCTCCCCACCCCATTGAGC
GCCTGCACCACATGCACATCTACCCTATCGTCATCTTCATCCACTACAAGAGTGCCAAGCACATCAAGAAGCAGAGAGAC
CCCATCTACTTGAGGGGCAAGGTGACACAGAGGCATTCCAAAGAGCAGTTCAAAACAGCTCAGAAGACGGAACAGGAGTA
CAGCAGGTACTTCACAAGGGTCGTCCAGGGAGGAGCCCTGTCAAGCATTTGCACTTAGATCTTGGCAACCGTCAATCAAG
AACAAAGTAAAGTCCTGTGGATCCTCAACTGCCTGCTC

Alignment

ORF - retro_itri_1904 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.67 %
• Parental protein coverage: 59.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKSQLDLGVHLCGGNLHGVFVAEVEDDSPARGPDGLVPGDLILEYGNLDVRNKTVEEVYVEMLKPKDSVR
          KKSQLD.GVHLCGGNLH.VFVAEVEDDSPARGPDGLVPGDLILEYGNLDV.NK.V.EVYVEMLKPKDS.R
Retrocopy KKSQLDFGVHLCGGNLHRVFVAEVEDDSPARGPDGLVPGDLILEYGNLDVHNKMVDEVYVEMLKPKDSIR

Parental  LKVQYRPEEFTRIKGLPGDSFYIRALYDRLAEVEHELSFRKDDIL-YVDDTLPQGTFGSWMAWQLDENAQ
          LKV.YRPEEFTRIKGLPGDSFYIRALYDRLAEVEHELSFRK.DIL..VDDTLPQGTFGSWMAW.LDENAQ
Retrocopy LKV*YRPEEFTRIKGLPGDSFYIRALYDRLAEVEHELSFRKEDIL<LVDDTLPQGTFGSWMAWHLDENAQ

Parental  KIQRGQIPSKYVMDQEFSRRLSMSEVKDDSNAAKTLSAAARRSFFRRKHKHKRSGSKDGKDLLALDTFSN
          .IQR..IPSK.VMDQEFS.RLSMSEVKD.S.A.KTLSAAA..SFF.RKHKHK..GSKD.KDLLALDTFSN
Retrocopy NIQRWHIPSKCVMDQEFSMRLSMSEVKD-SSATKTLSAAACWSFFGRKHKHKCNGSKDRKDLLALDTFSN

Parental  DSLPLFEGKLSLAYQRVQKVDCTSLRPVLILGPLLDVVKEMLINEAPGKFCRCPLEVMKASQQAIERGVK
          DSL.LFE...SLAYQ.VQKVDC.SLRPVLILGPLLD.VKEMLINE.PGKFCRCPL.VMKASQQAIERG.K
Retrocopy DSL*LFEDSVSLAYQQVQKVDCISLRPVLILGPLLDMVKEMLINEVPGKFCRCPLKVMKASQQAIERGIK

Parental  DCLFVDYKRRSGHFDVTTVASIKEITEKNRHCLLDVAPHAIERLHHMHIYPIVIFIHYKSAKHIKEQRDP
          DCLFVDYKRR.GHFDVT.VASIKEITEKNRHCLLDVAPH.IERLHHMHIYPIVIFIHYKSAKHIK.QRDP
Retrocopy DCLFVDYKRRNGHFDVTMVASIKEITEKNRHCLLDVAPHPIERLHHMHIYPIVIFIHYKSAKHIKKQRDP

Parental  IYLRDKVTQRHSKEQFETAQKIEQEYSRYFTGVVQGGALSSICTQILATVNQEQSKVLWIPACPL
          IYLR.KVTQRHSKEQF.TAQK.EQEYSRYFT.VVQGGALSSICT.ILATVNQEQSKVLWI..C.L
Retrocopy IYLRGKVTQRHSKEQFKTAQKTEQEYSRYFTRVVQGGALSSICT*ILATVNQEQSKVLWILNCLL

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_1904 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1904 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000022087	1 retrocopy	retro_itri_1904 ,