RetrogeneDB ID: retro_itri_1403

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393476.1:3388783..3389536(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000007924
• Aliases: None
• Description: None

Sequence

>retro_itri_1403
CTAGCTACAGCAAGTAAACAAAATACTTTGATTTAAATCTCTTTTGGAAGAAGATGTAGAAGAAAAAAGCCTATAAAAAT
CAAGTTGAGGAATCTGCTAAACATATACAAGTTCTTCAAGCCTATCTGCAGAAATTACACATTGCCATAGAGAATCTCCA
GGAAGAGAAAGACCATAAAATCATAAGCACTAGAGATGAATTGCTTAGCTGCCGAGATGAAATTTTGCTGCTTCACGAGG
CAGCTGCACAGGCTGCTTCTGAGCAGGACACTGACATTACTTCTTTACAAGATGAGTTTAAGTAGGTGCCAGCTGAAGTG
TGAGTGGTGGTGGTGGTGGACAGTGGCACCTGAGTATGAGATAGAAATCACAAGTCTGTAGAACAGTTTTCAGCTTTGGT
GTCAACAGTATGAAGACCAGCGGAGAGCAGAAGCAACAAGGTTGCTAGGTGAACTAGAGAAGTTGAAAAAGGAAGGGAAT
GTATTGGAAACCGAGTGCCCTTCTCTAAATGTTTTGCTATCATCAGAACTGCAGTGGCAAGAAAAAGAAATATGCAATTC
TGAGAAACAGAGTTTAGAGTTTACCAGTGATCACAGCATCCTTCAGGTGACTAGGAAAGAACTGGAGAACCAAGTGGGAT
CCTTGAAAGAGCAGCATCTTCAGGATTCAGCGGATTTAAAAACTCTTCTCAGTAAGGCTGAAAACCAAGCAAAGGATGTA
CAGAAAGTCTGAAGAGACACAGACTGCACCCTC

Alignment

ORF - retro_itri_1403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.09 %
• Parental protein coverage: 72.05 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LARASKQ-KCFELQALLEE--ERKAYRNQVEESAKQIQVLQGQLQRLHIDIENLREEKDGEITSTRDELL
          LA.ASKQ.K.F.L..........KAY.NQVEESAK.IQVLQ..LQ.LHI.IENL.EEKD..I.STRDELL
Retrocopy LATASKQ<KYFDLNLFWKKM*KKKAYKNQVEESAKHIQVLQAYLQKLHIAIENLQEEKDHKIISTRDELL

Parental  SARDEILLLHQAAAKAASERDTDIISLQDELKKVRAEL-ERWRKAASEYEKEI--TSLQNSFQLRCQQCE
          S.RDEILLLH.AAA.AASE.DTDI.SLQDE.K.V.AE..E.W.......E.EI..TSL.NSFQL.CQQ.E
Retrocopy SCRDEILLLHEAAAQAASEQDTDITSLQDEFK*VPAEV>EWWWWWTVAPEYEIEITSL*NSFQLWCQQYE

Parental  DQQRVEATRLQSELEKLRKEWNVLETECHSLKKENVLLSSELQRQEKELHNSQKQSLELTSDLSILQMTR
          DQ.R.EATRL..ELEKL.KE.NVLETEC.SL...NVLLSSELQ.QEKE..NS.KQSLE.TSD.SILQ.TR
Retrocopy DQRRAEATRLLGELEKLKKEGNVLETECPSL---NVLLSSELQWQEKEICNSEKQSLEFTSDHSILQVTR

Parental  KELENQVGSLKEQHLRDSADLKTLLNKAENQAKDVQKEYEKTQTVL
          KELENQVGSLKEQHL.DSADLKTLL.KAENQAKDVQK....T...L
Retrocopy KELENQVGSLKEQHLQDSADLKTLLSKAENQAKDVQKV*RDTDCTL

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_1403 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1403 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	ENSSTOG00000007924	1 retrocopy	retro_itri_1403 ,