RetrogeneDB ID: retro_itri_830

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393330.1:6157971..6158812(+)
• Located in intron of: ENSSTOG00000002303

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCTN4
• Ensembl ID: ENSSTOG00000013446
• Aliases: None
• Description: dynactin 4 (p62) [Source:HGNC Symbol;Acc:15518]

Sequence

>retro_itri_830
GACAAATATGGTCTTGGAACCAGGCTTCAGCAACCACAAGCTAGTGCATCCATCAGTACCCTTGCTGGGCTTTCCCTTAA
AGAAGGAGAGGACCAGAAAGAGATAAAGATTGAGCCAGCTCAGGCCATGGATGAAGTGGAACTTCTACCTGAAAACTATT
ACACAGGACCAGTAAATTTAAAAGAGGTGACTACCCTTCAGCAGCGCCTCTTACAGCCTGACTTCCAACCAATTTGTGCT
TCACGACTCTATCCTCGTCACAAACATCTTCTGATCAAACGGACCCTGCACCACTGAAAATGTGAACATAATTTGAGCAA
GCCTGAATTTATTCCAACATCTGTCAAATTCAAAATCCAACTGGTTGCTGTCAATTATATTCCAGAAGTGAGAATCGTGT
CAATTCCCAACCTTTGCTACATGAAGGAGAGCCAGGTCCTTCTGACTCTTTCGAATCCTGTGGAAAACCTTACCCATGTG
ATTCTGTTTCCAGAGTGTGAGGTGGGAGTCCTGATGATATCAGTAGCACTGGTAAGGTGGTAGTGTCTCCCAAAGAGCTC
ATTTTAGCTGGCAAGGATGCAGCAGCAGAATATGATGAGTTGGCAGAACCCCAGGATTTTCAGGATGATCCTGACATTAT
AGCCTTCAGAAAGGCCAACAAAGCGGGCATTTTCATCAAAGTTACCCCCCAACGTGAGGAGGGTAAAGTGACCGTGTTCT
TTAAGATGAAGCATGATTTTAAAAACCTGGCAGCCCCAATTTGCCCCATTGAAGAAAGTGACCAGAGCACAGAATTATCT
GGCTCACCCAGCATGTGGAACTCAGGTTGGGCCCATTTCTT

Alignment

ORF - retro_itri_830 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.99 %
• Parental protein coverage: 59.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DKYGLGTRLQRPRAGASISTLAGLSLKEGEDQKEIKIEPAQAVDEVEPLPEDYYTRPVNLTEVTTLQQRL
          DKYGLGTRLQ.P.A.ASISTLAGLSLKEGEDQKEIKIEPAQA.DEVE.LPE.YYT.PVNL.EVTTLQQRL
Retrocopy DKYGLGTRLQQPQASASISTLAGLSLKEGEDQKEIKIEPAQAMDEVELLPENYYTGPVNLKEVTTLQQRL

Parental  LQPDFQPICASQLYPRHKHLLIKRSLRCRKCEHNLSKPEFNPTSIKFKIQLVAVNYIPEVRIMSIPNLRY
          LQPDFQPICAS.LYPRHKHLLIKR.L...KCEHNLSKPEF.PTS.KFKIQLVAVNYIPEVRI.SIPNL.Y
Retrocopy LQPDFQPICASRLYPRHKHLLIKRTLHH*KCEHNLSKPEFIPTSVKFKIQLVAVNYIPEVRIVSIPNLCY

Parental  MKESQVLLTLTNPVENLTHVTLF-ECE-EGDPDDINSTAKVVVPPKELILAGKDAAAEYDELAEPQDFQD
          MKESQVLLTL.NPVENLTHV.LF.ECE..G.PDDI.ST.KVVV.PKELILAGKDAAAEYDELAEPQDFQD
Retrocopy MKESQVLLTLSNPVENLTHVILFPECE<GGSPDDISSTGKVVVSPKELILAGKDAAAEYDELAEPQDFQD

Parental  DPDIIAFRKANKVGIFIKVTPQREEGEVTVSFKMKHDFKNLAAPIRPIEESDQSTE-VIWLTQHVELSLG
          DPDIIAFRKANK.GIFIKVTPQREEG.VTV.FKMKHDFKNLAAPI.PIEESDQSTE..IWLTQHVEL.LG
Retrocopy DPDIIAFRKANKAGIFIKVTPQREEGKVTVFFKMKHDFKNLAAPICPIEESDQSTE<IIWLTQHVELRLG

Parental  PLL
          P.L
Retrocopy PFL

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_830 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_830 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000014234	1 retrocopy	retro_pvam_334,
Rattus norvegicus	ENSRNOG00000019298	1 retrocopy	retro_rnor_1305,
Ictidomys tridecemlineatus	ENSSTOG00000013446	1 retrocopy	retro_itri_830 ,