RetrogeneDB ID: retro_pmar_19

Retrocopy location

• Organism: Lamprey (Petromyzon marinus)
• Coordinates: GL492575:420..1320(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: has1
• Ensembl ID: ENSPMAG00000005470
• Aliases: None
• Description: hyaluronan synthase 1 [Source:ZFIN;Acc:ZDB-GENE-040218-2]

Sequence

>retro_pmar_19
CAGATCCTCAACCGGTACGCGTCGCTGCTCGCCTTCCTGAGCAGCGTGCGCTACTGGGTGGCCTTCAACGTGGAGCGCGC
CTGCCAGTCCTACTTCGGCTGCGTGCAGTGCATCAGCGGCCCCCTGGGCCTCTACCGCAGCTCGCTCGTTCGTGAGATCC
TCGAGGCCTGGTACGGGCAGCGCTTCCTCGGCTCGCCGTGCAGCTTCGGCGACGACCGCCACCTCACGAACCGCGTGCTC
GGCCTCGGCTTCTCCACCAAATACACGGCGCGCGCGCGCTGCCTGACCGAGACCCCCGCGGGCTATCTGCGCTGGCTCAA
CCAGCAGACGCGCTGGAGCAAGTCCTACTTCAGGGAGTGGCTCTACAGCGCCACGTGCTTCCACAAGCACCACCTGTGGA
TGACTTACGAGGCGGTCGTCACGGGCTTCTTCCCCTTCTTCCTGGCCACCACGGTGGTGCAGCTCTTCTACCGCGGCAGC
GCATGGGCCATCCTTACCTTCCTGCTCATCGTGCAGGTGGTGGCGCTGCTCAAGGCCGGCGTCGCGTGCGCCCTGCGCGG
CCGCGTCGTCATGATCTTCATGTCGCTCTACTCGCTCCTCTACATGAGCAGCCTCCTGCCGGTCAAGATTTGCGCCTTGG
CCACCGTCAGCAGCGCCGGTTGGGGCACCTCGGGCAGGCGGACGATGGTCACCAACCTCGCCGGGCTCGTGCCCGTGCTC
GTCTGGGCCGCCGTGCTGGCCGGCGGCGTGGTTCGCACGGTGAACAAGGAGATGGCCTCGCCTCCGGCCCCGTCGGAGCG
GTCTTTGGTGTGGGCCGGCGCGGCGCTGTACGCGAGCTTCTGGGCCGTGCTCATGGCCCTGTACCTGGGGCTCGTGGCCA
GGTGGTGCTGTCGAGGGAGA

Alignment

ORF - retro_pmar_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.33 %
• Parental protein coverage: 54.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RILNLNDSYISFMSNLRYWMAFNVERSCQSYFDCVSCISGPLGLYRNVLLQQFMESWYNQKFLGTHCTFG
          .ILN...S...F.S..RYW.AFNVER.CQSYF.CV.CISGPLGLYR..L.....E.WY.Q.FLG..C.FG
Retrocopy QILNRYASLLAFLSSVRYWVAFNVERACQSYFGCVQCISGPLGLYRSSLVREILEAWYGQRFLGSPCSFG

Parental  DDRHLTNRMLSMGYATKYTSRSICYSETPAQYLRWLNQQTRWTKSYFREWLFNAMWWHKHHLWMTYESTV
          DDRHLTNR.L..G..TKYT.R..C..ETPA.YLRWLNQQTRW.KSYFREWL..A...HKHHLWMTYE..V
Retrocopy DDRHLTNRVLGLGFSTKYTARARCLTETPAGYLRWLNQQTRWSKSYFREWLYSATCFHKHHLWMTYEAVV

Parental  AGIFPFFVTATVIKLFYTGSIWDILWVLCAIQIIGFIKSLYACWLRGNLVMVFMSLYSVLYMTSLLPTKY
          .G.FPFF...TV..LFY.GS.W.IL..L...Q.....K...AC.LRG..VM.FMSLYS.LYM.SLLP.K.
Retrocopy TGFFPFFLATTVVQLFYRGSAWAILTFLLIVQVVALLKAGVACALRGRVVMIFMSLYSLLYMSSLLPVKI

Parental  FAIITMNKSSWGTSGRKKMVGNYIPLLPLSIWAAILFGGIAFAIYHETQVNHSEEDKKYLIYGSVAYVLF
          .A..T.....WGTSGR..MV.N...L.P...WAA.L.GG.......E...............G...Y..F
Retrocopy CALATVSSAGWGTSGRRTMVTNLAGLVPVLVWAAVLAGGVVRTVNKEMASPPAPSERSLVWAGAALYASF

Parental  WIIMIISYWVFI-RKCCRNR
          W......Y.....R.CCR.R
Retrocopy WAVLMALYLGLVARWCCRGR

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_19 retrocopy.

TSS

Petromyzon marinus was not studied using FANTOM5 data.

Lab

retro_pmar_19 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	ENSPMAG00000005470	1 retrocopy	retro_pmar_19 ,