RetrogeneDB ID: retro_itri_996

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393357.1:1973033..1973847(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000015265
• Aliases: None
• Description: None

Sequence

>retro_itri_996
GAGGATGTCCCTAAATCACGTACTAGTTGCAACTCTCACTGTTCAAGTTCCAGACAGTATTCTAAGAACACAAGTCCAGA
ATCTGAAACAGAATATATATTTTGGGAAGACTTGTTACATTGTGCAGAATGCCATTTATCTTGTACCAGTGAGACAGATG
TGGAAAATCCTCAAATTATTCCATGTGTGAAAACATAATATGGAGACGACTATTTTCATTAGAATCATTTGCCCTGGCTT
CATAGGTCCCCCTCAGAATTAGAAAAATAAGTGCTATAGTATAGGAAGGCAAAGACTGTAAAAAAGCAGAAATGTCTGTA
CTTGAAATCAGTGTAATGATAATGAACAGAGTGATCAGCCATATACGAGGAATAGGATACCAGAGTTTTGGAAATGTAAT
CTCTCTAATCCTGGGTTTAATCCCATTTGTTTTTTGACTTTCTCAAGCTACAGACTTGAAACAACTCACAGCACATTCTG
CTTCAGAAGTTTATGTGATTTCATTTGGTTTTAATGAAGATGTCATGGTTCTTTTTATGGTTATAATATGTTTTGTGGTC
CATATCTCTATTGTATGGACTTTCTTTTTCTTGCTCTGTGTAGCAAAAAGAACTTATTAATAGCAACTACTTTTTGCAAA
ACTCTTTGGATATTTAATAGCTACAAAGAAGGCACAGCAATCTGAGATTCCTCATTTCTGGCTGAAGAAAGTATAGATAT
AAAAATGTGGCTATCTCTCTGTCCCTGTGTTAAGTGTTGAGGTCCTCAGAGATCAGTTGATGTAATAGTATCATCTGACT
ATCTCAGTTGTATT

Alignment

ORF - retro_itri_996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.36 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QDAPKSGTSCSSRCSSSRQDSESTRPESETEDILWEDLLHCAECRSSCTSETDVENPQINPCVKKEYRDD
          .D.PKS.TSC.S.CSSSRQ.S..T.PESETE.I.WEDLLHCAEC..SCTSETDVENPQI.PCVK..Y.DD
Retrocopy EDVPKSRTSCNSHCSSSRQYSKNTSPESETEYIFWEDLLHCAECHLSCTSETDVENPQIIPCVKT*YGDD

Parental  PFHQSHVPWLHSSHPGLEK-ISAIVWEGNDCKKADMSVLEISGMIMNRVNSHIPGIGYQIFGNIISLILG
          .FH..H.PWLH.S...LEK.ISAIV.EG.DCKKA.MSVLEIS.MIMNRV.SHI.GIGYQ.FGN.ISLILG
Retrocopy YFH*NHLPWLHRSPSELEK<ISAIV*EGKDCKKAEMSVLEISVMIMNRVISHIRGIGYQSFGNVISLILG

Parental  LTPFVFRLSQATDLEQLTAHSASELYVIAFGSNEDVMVLSMVIISFVVRVSLVWIFFFLLCVAERTYKQR
          L.PFVF.LSQATDL.QLTAHSASE.YVI.FG.NEDVMVL.MVII.FVV..S.VW.FFFLLCVA.RTY...
Retrocopy LIPFVF*LSQATDLKQLTAHSASEVYVISFGFNEDVMVLFMVIICFVVHISIVWTFFFLLCVAKRTY**Q

Parental  LLFAKLFGHLTSARRARKSEVPHFRLKKV-QNIKMWLSLRSYLKRRGPQRSVDVIVSSAFLLTI
          LLFAKLFG.L.....A..SE.PHF.LKKV...IKMWLSL....K..GPQRSVDVIVSS..L..I
Retrocopy LLFAKLFGYLIATKKAQQSEIPHFWLKKV<IDIKMWLSLCPCVKC*GPQRSVDVIVSSDYLSCI

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_996 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_996 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000015265	1 retrocopy	retro_itri_996 ,