RetrogeneDB ID: retro_pmar_13

Retrocopy location

• Organism: Lamprey (Petromyzon marinus)
• Coordinates: GL476660:240429..240630(-)
• Located in intron of: ENSPMAG00000005127

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPMAG00000005110
• Aliases: None
• Description: Variable lymphocyte receptor B cassette [Source:UniProtKB/TrEMBL;Acc:A5HHB2]

Sequence

>retro_pmar_13
CAAATAACGGACTGTGATGGCAAAGGACCGAGTTCAGTTACATCTGGAATTGCCGACAGCACCCACGTCTTGGATTTGAG
AAGCAATCGCATAAAAAGTCTCGCCGAGGGGGTGTTTAACCCAGTGGGGTCTCACCCCCCTAATGAGTTGCTGACTCTCA
CCTGGTTAATTAAAGGACGCCTTATGATCACCAATTTAGAC

Alignment

ORF - retro_pmar_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.11 %
• Parental protein coverage: 72.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QTTDCDGKGLSSVPSGIPDNTQNLDLRKNQIDRLPEGVFNPVSNQAHLAANEMTALPARVFNKLTQLTRL
          Q.TDCDGKG.SSV.SGI.D.T..LDLR.N.I..L.EGVFNPV........NE...L.......L...T.L
Retrocopy QITDCDGKGPSSVTSGIADSTHVLDLRSNRIKSLAEGVFNPVGSH---PPNELLTLTWLIKGRL-MITNL

Parental  D
          D
Retrocopy D

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_13 retrocopy.

TSS

Petromyzon marinus was not studied using FANTOM5 data.

Lab

retro_pmar_13 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	ENSPMAG00000005110	1 retrocopy	retro_pmar_13 ,