RetrogeneDB ID: retro_itri_1828

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393932.1:36328..37090(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000011569
• Aliases: None
• Description: None

Sequence

>retro_itri_1828
CAGGAGTACAAAACTATCTACCTAGAGGGCCTTCCACCACTCCTTGAGTATGAATTGGCCCCATCCAAGTTACAAGAGGA
GGTGGATGATATTTATCTCATTGGAGCTGAAGGATTGCCTTGGTCATGTACTGTGGAAGATGTGCTTAAGTTTTTCTCAG
ACTGCAGAATCCACAATAGTGAGAATGGAATACATTTCCTTTTAAATAGAGTTGAAAAACAAAGGGGTGATGCCTTAGTT
GAAATGGAGTCAGAGAAGGATGTGCAGAAAGCCTAAGAAAAGCACTGCATGTACATGGGTAAGTGATATGTGGAAGTATA
TGAGATAAAAAATGATGATGGAGATGCCTTAATGAAGAGCCTACAGGTCAAATCATCACCTGTGGTGAATGATGGTGTAG
TTCGTTTAAGAGGATTTTCTTATCGTTGCAATAAGAAAGACATCATAGACTTCTTTGCAGGACTGAATACAGTGGACATT
ATTTTGTGATAGCGTATAAAGGTAGAAGAAAAACATGGAAAGCATATGTGCAGTTTGAAGAACCAGAAATGGCCAACCAA
GCCTTGTTGAAACACAGGGAAAAAATGGTAACTGATATACAGAGTTATTTCTAGCAGAAGGAATAAAGTTCGAACCCATG
TTGGCTCTCATAAGGGAAAGAAAATGGCATCTTCTGCTACTGCTAAGTATATAACTAAGCCAGAAATTATCTTTGAAGAA
CATGAAGTAAATGAGGACATTATACCCATGACAGGTTTTGAA

Alignment

ORF - retro_itri_1828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.23 %
• Parental protein coverage: 54.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KESKTTYLEDLPPLPEYELAPSKLGEEVDDVYLIRAQGLPWSCTVEDVLNFFSDCRIRNSENGIHFLLNR
          .E.KT.YLE.LPPL.EYELAPSKL.EEVDD.YLI.A.GLPWSCTVEDVL.FFSDCRI.NSENGIHFLLNR
Retrocopy QEYKTIYLEGLPPLLEYELAPSKLQEEVDDIYLIGAEGLPWSCTVEDVLKFFSDCRIHNSENGIHFLLNR

Parental  DGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVYEINNEDVDALMKSLQVKSSPVVNDGVVRLRGLP
          ..K.RGDAL.EMESE.DVQKA.EKH.MYMG..YVEVYEI.N.D.DALMKSLQVKSSPVVNDGVVRLRG..
Retrocopy VEKQRGDALVEMESEKDVQKA*EKHCMYMGK*YVEVYEIKNDDGDALMKSLQVKSSPVVNDGVVRLRGFS

Parental  YSCNEKDIVDFFAGLNIVDIT-FVMDYRGRRKTGEAYVQFEEPEMANQALLKHREEI-GNRYIEIF-PSR
          Y.CN.KDI.DFFAGLN.VDI..FV..Y.GRRKT..AYVQFEEPEMANQALLKHRE...GN.Y.E.F..SR
Retrocopy YRCNKKDIIDFFAGLNTVDII<FVIAYKGRRKTWKAYVQFEEPEMANQALLKHREKM<GN*YTELF<SSR

Parental  RNEVRTHVGSHKGKKMASSPTAKYITEPEMVFEEHEVNEDIRPMTSFE
          RN.VRTHVGSHKGKKMASS.TAKYIT.PE..FEEHEVNEDI.PMT.FE
Retrocopy RNKVRTHVGSHKGKKMASSATAKYITKPEIIFEEHEVNEDIIPMTGFE

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_1828 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1828 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000007721	1 retrocopy	retro_nleu_1973,
Ictidomys tridecemlineatus	ENSSTOG00000011569	2 retrocopies	retro_itri_1828 , retro_itri_523,
Ictidomys tridecemlineatus	ENSSTOG00000011676	1 retrocopy	retro_itri_647,
Ictidomys tridecemlineatus	ENSSTOG00000016376	2 retrocopies	retro_itri_66, retro_itri_78,
Tupaia belangeri	ENSTBEG00000010173	2 retrocopies	retro_tbel_3827, retro_tbel_987,
Tarsius syrichta	ENSTSYG00000008487	1 retrocopy	retro_tsyr_770,