RetrogeneDB ID: retro_itri_1854

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394129.1:73393..73902(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STX3
• Ensembl ID: ENSSTOG00000007206
• Aliases: None
• Description: syntaxin 3 [Source:HGNC Symbol;Acc:11438]

Sequence

>retro_itri_1854
CGCTCATCAGCAGGCCTTCTCTCTGGGAAGTCTGTGGAGGCGATGACCAGGTACAATGAGGCTCGGGGGGACTTCGTGAA
CACAGCCAAGGGCGAACCCAGGCAGCTGGAGATTACTGGCAACAAGACAAGGCAGAGGAGCAGGAGGAGATGCTGCCGAG
TGGCTGCCTGCCATCTCACTTCTGGGATCACCGACTCCCAGATTCCCAAGCAAGCCGTCAGGGAGACCGAGGGTGGGCAT
AAGGACATTGGGAGGCTGGAGAACAGCCTTAAAGAACTGCCTGACACGTGTATGGACAGTGCCAGGCTGGTGGAGGACCA
GGGCCAGAGATTAGATGGCCTAGAGCTGGACGTCATGCACACAGTGGACCGTGTGAGAAGGCACGAGACGAAACTCCAAG
AGCTGTGAACTACCAGGGTCAGGCCCGGGAGAAATCGGTGACCATCACTGTGATGGTGGTCGTGCTGCTGGGCACCTTAG
CCTCCATCCCTGGACTTGCCGTTGGGCTG

Alignment

ORF - retro_itri_1854 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.77 %
• Parental protein coverage: 59.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KSQHSVLSRKFVEVMTKYNEAQVDFRERSKGRIQRQLEITGKKTTD-EELEEMLESGN-PAI-FTSGIID
          .S....LS.K.VE.MT.YNEA..DF....KG...RQLEITG.KT...EE.EEML.SG..PAI..TSGI.D
Retrocopy RSSAGLLSGKSVEAMTRYNEARGDFVNTAKGE-PRQLEITGNKTRQ<EEQEEMLPSGC<PAI<LTSGITD

Parental  SQISKQALSEIEGRHKDIVRLESSIKELHDMFMDIAMLVENQGEMLDNIELTVMHTVDHV-EKARDETKR
          SQI.KQA..E.EG.HKDI.RLE.S.KEL.D..MD.A.LVE.QG..LD..EL.VMHTVD.V.EKARDET.R
Retrocopy SQIPKQAVRETEGGHKDIGRLENSLKELPDTCMDSARLVEDQGQRLDGLELDVMHTVDRV<EKARDETPR

Parental  AVKYQGQARKKLIIIIVIVVVLLGILALIIGLSVGL
          AV.YQGQAR.K...I.V.VVVLLG.LA.I.GL.VGL
Retrocopy AVNYQGQAREKSVTITVMVVVLLGTLASIPGLAVGL

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_1854 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1854 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000026681	1 retrocopy	retro_mluc_105,
Ictidomys tridecemlineatus	ENSSTOG00000007206	1 retrocopy	retro_itri_1854 ,