RetrogeneDB ID: retro_itri_1012

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393358.1:6660534..6660930(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STMN2
• Ensembl ID: ENSSTOG00000025094
• Aliases: None
• Description: stathmin-like 2 [Source:HGNC Symbol;Acc:10577]

Sequence

>retro_itri_1012
GAATTGAAGCAAATCAGCAGGTCTGCCCCCAGCCAGGCATTTGAGCTGATCTTAATGCCTCCATGTCCTATCTCAGAAGT
CCAAAGAATTCTTGTTTCTCCAAAGGAGAAAACCCTGTCCTAGATGAGGTCCAGGAAAAAGTAGAGGCTGCAGAGGAAAG
AAAGTCTCAGGAGGCCCAGGTGCTGAAGCAATTAAGAGAGAAGAAAGAACAAGAGCAAAAAAGTCCCTCGGAGGCTTTGG
AGGAAAGCAACAACTTCAGCAAGATGGTAGAACAAAAACTGACCTTGAAAATGGAACACATTAAGAAAAACTTTGAGGCT
AACTAGCTGCTATTATTAAGTATCTGCAGAAAAAGGAGAAGCATGTGTTGAAGGTGCCAGGAACAAGGAACTCCAG

Alignment

ORF - retro_itri_1012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.42 %
• Parental protein coverage: 95.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EVKQINKRASGQAFELILKPPSPISEAPRTLASPKKKDLS-LEEIQKKLEAAEERRKSQEAQVLKQLAEK
          E.KQI...A..QAFELIL.PP.PISE..R.L.SPK.K.LS.L.E.Q.K.EAAEE.RKSQEAQVLKQL.EK
Retrocopy ELKQISRSAPSQAFELILMPPCPISEVQRILVSPKEKTLS<LDEVQEKVEAAEE-RKSQEAQVLKQLREK

Parental  REHEREVLQKALEENNNFSKMAEEKLILKMEQIKENREAN-LAAIIERLQEKERHAAEV-RRNKELQ
          .E.E......ALEE.NNFSKM.E.KL.LKME.IK.N.EAN.LAAII..LQ.KE.H...V..RNKELQ
Retrocopy KEQEQKSPSEALEESNNFSKMVEQKLTLKMEHIKKNFEAN<LAAIIKYLQKKEKHVLKV<ARNKELQ

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_1012 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1012 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
Dasypus novemcinctus	ENSDNOG00000003373	3 retrocopies	retro_dnov_2381, retro_dnov_545, retro_dnov_831,
Mustela putorius furo	ENSMPUG00000001863	1 retrocopy	retro_mputfur_68,
Otolemur garnettii	ENSOGAG00000027869	2 retrocopies	retro_ogar_2664, retro_ogar_330,
Oryzias latipes	ENSORLG00000008251	1 retrocopy	retro_olat_37,
Sorex araneus	ENSSARG00000010989	1 retrocopy	retro_sara_756,
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,
Tarsius syrichta	ENSTSYG00000014759	1 retrocopy	retro_tsyr_26,