RetrogeneDB ID: retro_itri_1662

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393616.1:379948..380499(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK16
• Ensembl ID: ENSSTOG00000025197
• Aliases: None
• Description: serine/threonine kinase 16 [Source:HGNC Symbol;Acc:11394]

Sequence

>retro_itri_1662
CTGTGTGTCTGCTCTCGTGGAACTGTCATCATTGACAATAAGCGTTACCTCTTCATCCAGAAACTGGGGGAGAGTGGGTT
CAGCTATGTGGCTAGTGGAGGGGTTACATGACAGACACTTCTACTCCCTGAAGAGAATCCTGTGTCAGGAGCAGGAGCAG
CAGGACCGGGAGGAGGCTCAGTGGGAAGCCAACATGCATTGCCTCTTTACTACCCCAACATTGTTTGCCTCTTGGCTTAC
TGTCTGAGAGAGTGTGGTGCTAAGCATGAGGCCCAGGTGCTGCTACCTTTCTTCAAGAGAGTTACGCTGTGGGATGAAAT
ATAAAGGCCGAAAGACAAAGGCAATTTCATGACTGGAGGATCAAATCCTTGGCTGCTGTTGGGTATCTGCAGAGGCATTG
AGGCCATTCATACCAAAGGTTTGCCCACAGGGACCTGAAGCCCACCAATATCTTGCTTGGAGATGAGAGGAAGCCAGTTT
TCATGGACTTGGGTTCCATGAATCAAATATGTATCCAAGTGGAGGGTTCCCGCCAAGCTCTGACCCTTCAG

Alignment

ORF - retro_itri_1662 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.95 %
• Parental protein coverage: 60.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LCVCSRGTVIIDNKRYLFIQKL-GEGGFSYVDLVEGLHDGHFYALKRILCHEQ--QDREEAQREADMHRL
          LCVCSRGTVIIDNKRYLFIQKL.G..G.S...LVEGLHD.HFY.LKRILC.EQ..QDREEAQ.EA.MH.L
Retrocopy LCVCSRGTVIIDNKRYLFIQKL>GRVG-SAMWLVEGLHDRHFYSLKRILCQEQEQQDREEAQWEANMHCL

Parental  F-HHPNILRLVAYCLKERGAKHEAWLLLPFFKRGTLWNEIERLKDKGNFLT-EDQILR-LLLGICRGLEA
          F...PNI..L.AYCL.E.GAKHEA..LLPFFKR.TLW.EI.R.KDKGNF.T.EDQIL..LLLGICRG.EA
Retrocopy F<YYPNIVCLLAYCLRECGAKHEAQVLLPFFKRVTLWDEI*RPKDKGNFMT>EDQILG<LLLGICRGIEA

Parental  IHTKG-YAHRDLKPTNILLGDEGQPVLMDLGSMNQACIQVEGSRQALTLQ
          IHTKG..AHRDLKPTNILLGDE..PV.MDLGSMNQ.CIQVEGSRQALTLQ
Retrocopy IHTKG<FAHRDLKPTNILLGDERKPVFMDLGSMNQICIQVEGSRQALTLQ

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_1662 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1662 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000000152	1 retrocopy	retro_dord_692,
Equus caballus	ENSECAG00000014093	1 retrocopy	retro_ecab_166,
Homo sapiens	ENSG00000115661	1 retrocopy	retro_hsap_1334,
Gorilla gorilla	ENSGGOG00000010907	1 retrocopy	retro_ggor_1040,
Macropus eugenii	ENSMEUG00000006422	1 retrocopy	retro_meug_1579,
Myotis lucifugus	ENSMLUG00000008066	1 retrocopy	retro_mluc_1213,
Pongo abelii	ENSPPYG00000013202	1 retrocopy	retro_pabe_1108,
Pan troglodytes	ENSPTRG00000012948	1 retrocopy	retro_ptro_911,
Ictidomys tridecemlineatus	ENSSTOG00000025197	2 retrocopies	retro_itri_1662 , retro_itri_602,