RetrogeneDB ID: retro_itri_1806

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393844.1:274826..275268(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STMN1
• Ensembl ID: ENSSTOG00000021708
• Aliases: None
• Description: stathmin 1 [Source:HGNC Symbol;Acc:6510]

Sequence

>retro_itri_1806
ATGGCTTCTTCTGATCTCCAGGTGAAAGAACTGGAGAAGCATGCCTCAGGCCAGACGTTTGAGCTGATTCTCAGTCCTCA
GTCAAAAGAATCCTTCCCAGATTTCCCCCCTTCCCCTCCAAAGAACAAGTATCTTTCTCTGGAGGAAATTCAGAAGAAAT
TAGAAGCTGAAGAAGAAAGATGCAAGTCCCATGAAACTGAGGTCTTGAAGCAGCTTGCTGAGAAATGACAGCATGAGAAA
GAAGTGCTTCAGAAAGCAACAGAAGAAAATAACACTTCATTAAAATGGAAGAGAAACTGACCCACAAACAGAGGCTAACA
AAGAGAACCAAGAGGCACAAGTGGCTGCCAAGCTGGAGCATTTTCAACAGAAGGATAAGCACATTGAAGAAGTGCAGAAG
AGCAAAGAATCCAAAGACCCTGCTGATGAGACTGAAGCTGAC

Alignment

ORF - retro_itri_1806 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASSDIQVKELEKRASGQAFELILSPRSKESVPDFPLSPPKKKDLSLEEIQKKLEAAEERRKSHEAEVLK
          MASSD.QVKELEK.ASGQ.FELILSP.SKES.PDFP.SPPK.K.LSLEEIQKKLEA.EER.KSHE.EVLK
Retrocopy MASSDLQVKELEKHASGQTFELILSPQSKESFPDFPPSPPKNKYLSLEEIQKKLEAEEERCKSHETEVLK

Parental  QLAEKREHEKEVIQKAIEENN-NFSKMAEEKLTHKM-EANKENREAQMAAKLERLREKDKHIEEVRKNKE
          QLAEK..HEKEV.QKA.EENN..F.KM.EEKLTHK..EANKEN.EAQ.AAKLE....KDKHIEEV.K.KE
Retrocopy QLAEK*QHEKEVLQKATEENN<HFIKM-EEKLTHKQ<EANKENQEAQVAAKLEHFQQKDKHIEEVQKSKE

Parental  SKDPADETEAD
          SKDPADETEAD
Retrocopy SKDPADETEAD

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_1806 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1806 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 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013761	1 retrocopy	retro_btau_247,
Callithrix jacchus	ENSCJAG00000009462	2 retrocopies	retro_cjac_3206, retro_cjac_474,
Cavia porcellus	ENSCPOG00000011075	1 retrocopy	retro_cpor_1505,
Loxodonta africana	ENSLAFG00000006089	1 retrocopy	retro_lafr_84,
Mus musculus	ENSMUSG00000028832	3 retrocopies	retro_mmus_1660, retro_mmus_2470, retro_mmus_3383,
Oryctolagus cuniculus	ENSOCUG00000006493	1 retrocopy	retro_ocun_56,
Ictidomys tridecemlineatus	ENSSTOG00000021708	5 retrocopies	retro_itri_1806 , retro_itri_1833, retro_itri_554, retro_itri_819, retro_itri_826,
Ictidomys tridecemlineatus	ENSSTOG00000025094	2 retrocopies	retro_itri_1012, retro_itri_1423,