RetrogeneDB ID: retro_itri_704

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393312.1:13503134..13503948(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000028402
• Aliases: None
• Description: None

Sequence

>retro_itri_704
ACATCACTTAGTCCTCTTACCCAGCTGATGAAAAAGATGCCCCATTTCTGTAAACAGATTACTAAGAAAATTGTCTATCC
TAATTTAGCAGAAGATTGCATGAATAAGTTCAAGCTTAATATAGAAAAGCTCTGTAAAACTGAACAGGACCTGGCACTTG
GAACTTATGCAGAAGGACAGAAGGTGAAAGATGCTATGAGAGTACTTCTTCCAGTTCTACTCAATAAAAATCATGATAAA
TGTGATAAAATAAGAGCAATCCTACTTTATATCTTCAGTACTAATGGAACTACAGAAGAATATTTGGACAGGTTGGTCCG
TAATGAAAAGATAGAAAATGAGAGTGACACGATTCATAACTGAAGTTATCTTGGTGTTCCCATTGTTCCCCAATCTCAAC
AAGGCAAAACCATTAAGAAAGGATTGGTCTGCAGAAGAAACTTTTCAACTTTCTTGATGGACACCTTTTATCAAAGATAT
TATGGAAGATGCCATTGATAATAGATTAGATTCAAAGGAATGGCCATATTGTTCTCAGTGTCCAGCAGTGTGGAATGGCT
CTGGAGCTGTAAGTACTTGCCAGAAACCTAGAACTAATTATTTAGAATTGGACCAAAAAAATGGATCAAAGCTGATTATT
TTTGTAACTGGAGGAATTACATATTCTGAAATTCACTGTGCTTATGAAGTTTCTCAGTTACATAAATCCTGTGAAGTTAT
TATTGGTTCTACACATATTTTAACACCCAAAAAGCTGTTGGATGATATAAAGATGCTGAATAAACCCAAGGATAAAGTCT
CCTTTACTAAAGAA

Alignment

ORF - retro_itri_704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSLSALTQLMKKMPHFRKQITKQVVHLNLAEDCMNKFKLNIEKLCKTEQDLALGTDAEGQKVKDAMRVLL
          TSLS.LTQLMKKMPHF.KQITK..V..NLAEDCMNKFKLNIEKLCKTEQDLALGT.AEGQKVKDAMRVLL
Retrocopy TSLSPLTQLMKKMPHFCKQITKKIVYPNLAEDCMNKFKLNIEKLCKTEQDLALGTYAEGQKVKDAMRVLL

Parental  PVLLNKNHDNCDKIRAILLYIFSTNGTTEENLDRLIQNVKIENESDMIRNWSYLGVPIVPQSQQGK-PLR
          PVLLNKNHD.CDKIRAILLYIFSTNGTTEE.LDRL..N.KIENESD.I.N.SYLGVPIVPQSQQGK.PLR
Retrocopy PVLLNKNHDKCDKIRAILLYIFSTNGTTEEYLDRLVRNEKIENESDTIHN*SYLGVPIVPQSQQGK>PLR

Parental  KDRSAEETFQLSRWTPFIKDIMEDAIDNRLDSKEWPYCSQCPAVWNGSGAVSARQKPRTNYLELDRKNGS
          KD.SAEETFQLS.WTPFIKDIMEDAIDNRLDSKEWPYCSQCPAVWNGSGAVS..QKPRTNYLELD.KNGS
Retrocopy KDWSAEETFQLS*WTPFIKDIMEDAIDNRLDSKEWPYCSQCPAVWNGSGAVSTCQKPRTNYLELDQKNGS

Parental  KLIIFVIGGITYSEMRCAYEVSQAHKSCEVIIGSTHILTPKKLLDDIKMLNKPKDKVSFTKE
          KLIIFV.GGITYSE..CAYEVSQ.HKSCEVIIGSTHILTPKKLLDDIKMLNKPKDKVSFTKE
Retrocopy KLIIFVTGGITYSEIHCAYEVSQLHKSCEVIIGSTHILTPKKLLDDIKMLNKPKDKVSFTKE

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_704 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_704 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	ENSSTOG00000028402	1 retrocopy	retro_itri_704 ,