RetrogeneDB ID: retro_itri_1287

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393428.1:3859531..3859954(-)
• Located in intron of: ENSSTOG00000009823

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000011783
• Aliases: None
• Description: None

Sequence

>retro_itri_1287
GCCATGACTGAGGCTGGAGGTTCTGAGGACTGCTGGCACATAGAAACTCAAAAAGAATTTGTTAAAGTCAGACAGAAAGA
CCTGGAACTGCTGACAAATGAAGCAATGCAAATATGGAATTTCTCACCCAGAATATCAAATGAGAAGTTACTGGAAAGTT
TCCAGAAATTAAATACTGTAGGAAAAACCCTAAAAAGAAAAGAGCAAGAGTAAGAACAGCTGAAACCAGATTGTGAGAAC
TTCAAAACTTGCCTGGAAACCATGCAGGCCAGAGATAAGAAGATCTCTCTTTGGCAGTAGCTGAAGAGAGCACAAACAGC
AGCTCCTAAAGCAGGCATAACATTGAACAAAAATGGGAGTGAGCCCTGCATCCTCCTGTGGGTTGTCTCCAACAGCAAGA
AAAGTATCTAAGTCATTCTGGGA

Alignment

ORF - retro_itri_1287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.39 %
• Parental protein coverage: 98.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AMGEAGGAEEACRHMGTKEEFVKVRKKDLERLTTEVMQIRDFLPRILNGEVLESFQKLKIVEKNLERKEQ
          AM.EAGG.E..C.H..T..EFVKVR.KDLE.LT.E.MQI..F.PRI.N...LESFQKL..V.K.L.RKEQ
Retrocopy AMTEAGGSED-CWHIETQKEFVKVRQKDLELLTNEAMQIWNFSPRISNEKLLESFQKLNTVGKTLKRKEQ

Parental  ELEQLKLDCEHFKARLETVQADSGREKKEKLALRQQLNEA-KQQLLQQAEYCTEMGAA-ACTLLWGVSSS
          E.EQLK.DCE.FK..LET.QA...R.K..K..L.Q.L..A.KQQLL.QA...T.MG....C.LLW.VS.S
Retrocopy E*EQLKPDCENFKTCLETMQA---RDK--KISLWQ*LKRA>KQQLLKQA*H*TKMGVS<PCILLWVVSNS

Parental  EEVVKAILG
          ......ILG
Retrocopy KKSI*VILG

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_1287 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1287 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000009866	1 retrocopy	retro_ogar_1556,
Sus scrofa	ENSSSCG00000022164	1 retrocopy	retro_sscr_868,
Ictidomys tridecemlineatus	ENSSTOG00000011783	1 retrocopy	retro_itri_1287 ,