RetrogeneDB ID: retro_pmar_17

Retrocopy location

• Organism: Lamprey (Petromyzon marinus)
• Coordinates: GL484055:4552..5156(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPMAG00000009051
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: trnt1
• Ensembl ID: ENSPMAG00000002236
• Aliases: None
• Description: tRNA nucleotidyl transferase, CCA-adding, 1 [Source:ZFIN;Acc:ZDB-GENE-040625-176]

Sequence

>retro_pmar_17
CTCGATGGGACACTTTACGGATACTTCAACGGAATGGAGGATCTGAAAAATAAGAGGGTGCGCTTCGTAGGAGACCCAGA
GAAAAGGATCCAGGAAGATTATCTCCGCATCCTGCGATATTTCAGGTTTTATGGATTCGTGGCCGAGCACGCGGACGCGA
GCCGCAGACGCTGGCGGCGATCGAGCGCGACGCGGGCGGGCGGGCTGGCCGGCATCGCGGGCGAGCGCATCTGGGTGGAG
CTGAAGAAGACACTCATGGGAAACCACGCGAGTCACCTCTTCGCTCTCATTTACAAGCTCGGCGTGGCACCACGCATAGG
CCTGCCATGCGACGGGAACGTGGGCGAGCTGCAGCGCGTGTGGGAGCGCTCGCGCGCCTCCGCCCCGCGCCCCATCACGC
TCCTGTCGGCGCTCCCGTGCTGCGCCGACGACGTGGGGCAGCTGGACGCGCGTCTCTGCCTCTCCAAGGACGAGCGCAAC
CTGGCGGCGTTCGTCATCAAGCACCGCGGGGAGCTGCGGCCCGCCGCGGACGGAGACGACCCCGCTCGGCTCCGTCAAGG
CCTTCGTCACCGAGGCGAAGGCGCACGCGAGCGAGCTGCCGCGC

Alignment

ORF - retro_pmar_17 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.66 %
• Parental protein coverage: 73.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LDGTLYDYFNGMEDLKNKKVRFVGDPEKRIQEDYLRILRYFRFYGSVAEHADAHEPQTLVAIERNAAGLA
          LDGTLY.YFNGMEDLKNK.VRFVGDPEKRIQEDYLRILRYFRFYG.VAEHADA............A.GLA
Retrocopy LDGTLYGYFNGMEDLKNKRVRFVGDPEKRIQEDYLRILRYFRFYGFVAEHADASRRRWRRSSATRAGGLA

Parental  GIAGERIWVELKKTLMGNHASHLFALIYKLGVAPHIGLPCDGNVGELQRVWERSRASAPRPITLLSALLR
          GIAGERIWVELKKTLMGNHASHLFALIYKLGVAP.IGLPCDGNVGELQRVWERSRASAPRPITLLSAL..
Retrocopy GIAGERIWVELKKTLMGNHASHLFALIYKLGVAPRIGLPCDGNVGELQRVWERSRASAPRPITLLSALPC

Parental  CADDVGHLDARLRLSKDERNLAAFVVKHRGELRPDADGDD-PLGSIKAFVTDARPHGEAKAR
          CADDVG.LDARL.LSKDERNLAAFV.KHRGELRP.ADGDD.PLGS.KAFVT.A..H.....R
Retrocopy CADDVGQLDARLCLSKDERNLAAFVIKHRGELRPAADGDD>PLGSVKAFVTEAKAHASELPR

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_17 retrocopy.

TSS

Petromyzon marinus was not studied using FANTOM5 data.

Lab

retro_pmar_17 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015466	1 retrocopy	retro_cjac_1512,
Dasypus novemcinctus	ENSDNOG00000008837	1 retrocopy	retro_dnov_1635,
Dipodomys ordii	ENSDORG00000014035	1 retrocopy	retro_dord_414,
Echinops telfairi	ENSETEG00000018177	2 retrocopies	retro_etel_1871, retro_etel_905,
Homo sapiens	ENSG00000072756	2 retrocopies	retro_hsap_246, retro_hsap_2598,
Gorilla gorilla	ENSGGOG00000015286	1 retrocopy	retro_ggor_300,
Nomascus leucogenys	ENSNLEG00000003226	1 retrocopy	retro_nleu_856,
Petromyzon marinus	ENSPMAG00000002236	1 retrocopy	retro_pmar_17 ,
Pongo abelii	ENSPPYG00000013702	3 retrocopies	retro_pabe_1916, retro_pabe_2721, retro_pabe_412,
Pan troglodytes	ENSPTRG00000014564	1 retrocopy	retro_ptro_1522,
Rattus norvegicus	ENSRNOG00000006432	1 retrocopy	retro_rnor_512,