RetrogeneDB ID: retro_itri_1574

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393551.1:1983780..1984595(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTMR9
• Ensembl ID: ENSSTOG00000020537
• Aliases: None
• Description: myotubularin related protein 9 [Source:HGNC Symbol;Acc:14596]

Sequence

>retro_itri_1574
TTCCTTCCTGAGCAAGAGTGTGAACTCTACTCTTCAGCTACCAGTGAATGAAGACTAAGCTATGGCAATAAGGAATTTGC
TATCTGCCCTTGCTATCTGACCAATTGTCATAGTGCCCAAATCCATTGATGATGCAGCTCTTCCAAAGGTACCTATATTG
GACACACAGGGTACATTCCATATTCAGCTATTCTCATTTTTTAAAAAATGAAATGGTAATTATGCAAAATGGTCAGTCAC
TCACTGGCACAAATGGGAGAAGGTACAAGGAAGATGAGACACTGATAAATGCTACCCTCAGGGCAGAAAACATGACTACA
TCATTGACACTTGTAGTCTGAATGTGGCTCAGCAAGCTAGAGCCAAAGGAGGTGACTTTGAACAGGAAGCCCATTACCCC
CAGTGGAGGCAATTTCATAAGTTCATTGAGAGGTATCACAGCCTAACCAAACTTGTGGAAGTTTGTGATGACCAAACATA
TAACATGGACCAATGGCTCAGTAAGTTGGAGGCCTCCAACTGGCTGACTCGTGGCAAAGAGATTCTGACCACTGCCTGTC
TAGCCACTCAGTGCATCCACAGGGAGGGAGCATCAGTCCTGATTCATGGAGCAGAAGGAACTGACTCTATCCTGCAGGCA
GCCTCCCTGGCTCAGTTCATTTTGGAACCACAGAGACAGATTGCCTGAGGTTTCAAGGCTCCAGACAGAAAGAGAGTGGC
TTCAGGCTGTTCACTCCTTCCAACACCACTGTGCACAGTCTGCCTATTGCAGTAGCAAGCAGAAGTGGCCAGCACCTGTA
GTTCTTCTCTTTTTG

Alignment

ORF - retro_itri_1574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.09 %
• Parental protein coverage: 50.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  FLPEQEFELYSSATSEWRLSYVNKEFAVCPSYP-PIVIVPKSIDDEALRKVATFR-HGGRFP-VLSYYH-
          FLPEQE.ELYSSATSE.RLSY.NKEFA.CP.Y..PIVIVPKSIDD.AL.KV.....H.G..P...SY.H.
Retrocopy FLPEQECELYSSATSE*RLSYGNKEFAICPCYL>PIVIVPKSIDDAALPKVPILD<HTGYIP<IFSYSHF

Parental  KKNGMVIMRSGQPLTGTNGRRCKEDEKLINATLRAG-KRGYIIDTRSLNVAQQARAKGGGFEQEAHYPQW
          .KN.MVIM..GQ.LTGTNGRR.KEDE.LINATLRA..K..YIIDT.SLNVAQQARAKGG.FEQEAHYPQW
Retrocopy LKNEMVIMQNGQSLTGTNGRRYKEDETLINATLRAE<KHDYIIDTCSLNVAQQARAKGGDFEQEAHYPQW

Parental  RRIHKSIERYHILQDSLIKLVEACNDQTHNMDRWLSKLEASNWLTHVKEILTTACLAAQCIDREGASVLI
          R..HK.IERYH....SL.KLVE.C.DQT.NMD.WLSKLEASNWLT..KEILTTACLA.QCI.REGASVLI
Retrocopy RQFHKFIERYH----SLTKLVEVCDDQTYNMDQWLSKLEASNWLTRGKEILTTACLATQCIHREGASVLI

Parental  HGAEGTDSTLQAASLAQIILEPRSRTVRGFEA-LIEREWLQAGHPFQQRCAQSAYCNSKQKWEAPVFLLF
          HGAEGTDS.LQAASLAQ.ILEP......GF.A...EREWLQA.H.FQ..CAQSAYC.SKQKW.APV.LLF
Retrocopy HGAEGTDSILQAASLAQFILEPQRQIA*GFKA>QTEREWLQAVHSFQHHCAQSAYCSSKQKWPAPVVLLF

Parental  L
          L
Retrocopy L

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_1574 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1574 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
Pan troglodytes	ENSPTRG00000019986	1 retrocopy	retro_ptro_2034,
Ictidomys tridecemlineatus	ENSSTOG00000008851	1 retrocopy	retro_itri_1894,
Ictidomys tridecemlineatus	ENSSTOG00000020537	1 retrocopy	retro_itri_1574 ,