RetrogeneDB ID: retro_pmar_22

Retrocopy location

• Organism: Lamprey (Petromyzon marinus)
• Coordinates: GL495798:3040..3442(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: iars
• Ensembl ID: ENSPMAG00000000527
• Aliases: None
• Description: isoleucyl-tRNA synthetase [Source:ZFIN;Acc:ZDB-GENE-030131-6325]

Sequence

>retro_pmar_22
GATGTTGTCACTAGATACGCAACTATGAAGGGTCATCACGTTGAGAGAAGATTTGGGTGGGATTGCCACGGTCTTCCAAT
CGAATACGAAATCGACAAGAAATACGAGATTAAGTCATCAATTCAAAGAGAAGAGATGGGAGTAAAAGAATATAACAGAA
GATGCAGAGAGATCGTTATGACATATTCTAAAGAATGGAAACACATTATCGGAAGATTCGGTCGTTGGATCGATTTCGAA
AATGACTACAAAACTATGGACTGCAATTTTATGGAGAGTGTATGGTGGACATTCAAGTAAATCTTTGACCAGGGATTGGT
TTATAGAGGTTCCAGAATCATGCCATTTTCCACTGGTTGCACTACAGTTTTATCAAACTTTGAAGCTGGTTCTAACTATA
AG

Alignment

ORF - retro_pmar_22 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.94 %
• Parental protein coverage: 67.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DVVTRFAHQSGFHVDRRFGWDCHGLPVEYEIDKMLNIKGPEDVAKMGIVEYNNQCRNIVMRYAKEWETTV
          DVVTR.A...G.HV.RRFGWDCHGLP.EYEIDK...IK.......MG..EYN..CR.IVM.Y.KEW....
Retrocopy DVVTRYATMKGHHVERRFGWDCHGLPIEYEIDKKYEIKSSIQREEMGVKEYNRRCREIVMTYSKEWKHII

Parental  IRLGRWIDFKNDYKTLYPSFMETVWWVFRQLFDKGFVYSGVKVMPYSTACTTPLSNFEANQNYK
          .R.GRWIDF.NDYKT....FME.VWW.F...FD.G.VY.G...MP.ST.CTT.LSNFEA..NYK
Retrocopy GRFGRWIDFENDYKTMDCNFMESVWWTFK*IFDQGLVYRGSRIMPFSTGCTTVLSNFEAGSNYK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Petromyzon marinus was not studied using RNA-Seq expression data.

ChIP-Seq

Petromyzon marinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pmar_22 retrocopy.

TSS

Petromyzon marinus was not studied using FANTOM5 data.

Lab

retro_pmar_22 was not experimentally validated.

Homology

Retrocopy orthology:

Petromyzon marinus 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
Petromyzon marinus	ENSPMAG00000000527	1 retrocopy	retro_pmar_22 ,