RetrogeneDB ID: retro_pmar_14

Retrocopy location

• Organism: Lamprey (Petromyzon marinus)
• Coordinates: GL476811:98389..98833(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NXPH3
• Ensembl ID: ENSPMAG00000002377
• Aliases: None
• Description: neurexophilin 3 [Source:HGNC Symbol;Acc:8077]

Sequence

>retro_pmar_14
GGCAAGTTCAAGAAGATGTTCGGCTGGGGAGACTTCAACTCCAACATCAAGACGGTGAAGCTCAACCTGCTCATCACGGG
CAAGATCGTGGACCACGGCAACGGCACGTTCAGCGTCTACTTTCGGCACAACTCGACCGGCCAGGGCAACGTGTCTCTGA
GCCTGGTGCCGCCCTCCAAGTCCGTGGACTTCGAGCCGTCCCCGGCGCAGTCGGCCGCTCTCGTGAACCCCAAGGAGACC
AAGTTCAATTGCCACGTGGAGTACGAGAAGACGGAGAAGTCCACGAAGACGGTGCTATGCATCTACGACCCGTCTCGCGT
CTGCTACCAGGAGCAGACGCAGAGCCACGTGTCGTGGCTGTGCGCAAAGCCCTTCAGCGTCATCTGCATCTACATCGCTT
TCTTCAGCACGGACTACAGACTCGTGCAGAAGGTGTGCCCGGAC

Alignment

ORF - retro_pmar_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.34 %
• Parental protein coverage: 94.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRPRKLFSWGDFSASIRTSRLQVLITAKMVDHGNGSVSVHFRHNATGRGSVSVSLGPPTVPLCLTPHRPL
          G...K.F.WGDF...I.T..L..LIT.K.VDHGNG..SV.FRHN.TG.G.VS.SL.PP.......P....
Retrocopy GKFKKMFGWGDFNSNIKTVKLNLLITGKIVDHGNGTFSVYFRHNSTGQGNVSLSLVPPSKSVDFEPSPAQ

Parental  TTESKAPRDGEPFRCRVEYEKVDRALKSVPCA-QPRSSCYREQVQSHVSWICSKPISAFCIYVAFQGANY
          ......P.....F.C.VEYEK.....K.V.C...P...CY.EQ.QSHVSW.C.KP.S..CIY.AF....Y
Retrocopy SAALVNPKETK-FNCHVEYEKTEKSTKTVLCIYDPSRVCYQEQTQSHVSWLCAKPFSVICIYIAFFSTDY

Parental  RLAHKVCPD
          RL..KVCPD
Retrocopy RLVQKVCPD

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_14 retrocopy.

TSS

Petromyzon marinus was not studied using FANTOM5 data.

Lab

retro_pmar_14 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	ENSPMAG00000002377	1 retrocopy	retro_pmar_14 ,