RetrogeneDB ID: retro_pmar_2

Retrocopy location

• Organism: Lamprey (Petromyzon marinus)
• Coordinates: GL482214:7860..8742(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPMAG00000010010
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: C1GALT1 (1 of 4)
• Ensembl ID: ENSPMAG00000001562
• Aliases: None
• Description: core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1 [Source:HGNC Symbol;Acc:24337]

Sequence

>retro_pmar_2
CCTCTCCGCCCCTCGCTGACGCTCCTCTTCGGCGTGAACGTCGGCTTCGGCCTGACCTACATCTTCCTGCTGGCCACGTC
GAACCTCGACGTGGCCGTGACTCCCCGTGAGCCGGCGCGACGCGACGCTCTGCGGGAGCTCCGCGCGCGCGTCCGCGTCC
TCTGCTGGGTCGTGACCTGCCCCCAGAACGTCGAGAGCAGGGCGCGACATCAGCGCGACACTTGGACCCGCGCCTGCGAC
CGCGTGCTCTTCCTGAGCTCCGTCGACGACGCGGAGTTCCCCGCCGTGGGGCTCGGCACCGAGGAAGGGCGCCAGCACCT
CTACTGGAAGACGACCAGGGCGATCCTCTACCTCCGCGAGCATCACGTCGACGACGCCGACTGGTTCTTGAAGGCGGACG
ACGACACTTACGTGCTGGTGGACAACCTCCGCCTCTTGCTGAGCGGTCACTCGGCCCGAAGTCCCGTCTACTTTGGCCGT
CGCTTCAAGGACCGACACAACAGGAGCTTCATGAGCGGTGGAGCCGGCTACGTGCTCAGCAGGGCCGCCCTCGTGCTGGC
TGCAGACGGCTTCGGGTCAGGTCAATGCGGGCAGGTCAGCCTGGCCGAGGACGTGGCCATTGGGGCGTGCTTGGAGAAGG
TCGGCGTGGCCTTTGGCGACTCGAGGGACTCGGCCGGCCGCGAGACCTTCCACCCGTTTGTGCCCGAAAAGCTCCTGGTG
CGTGACTTCATCTCCAACAACTCTTGGTACTGGAGGTATTGCTACCACCGGGCCGTGAGAGGTCCCCAGTGCTGTTCGGA
CTACCCCGTGTCTTTCCATTACGTGAGGCCGAGCTACATGCACGTTCTCGAGTACCTGGTGCATCGCCTTCGGCCGTACG
GC

Alignment

ORF - retro_pmar_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.35 %
• Parental protein coverage: 67.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQELRRRVRVLCWVMTGPQNLEKKARHLRATWTRACDKVLFMSSEEDKDLPAVGLHTKEGRDQLYWKTIR
          ..ELR.RVRVLCWV.T.PQN.E..ARH.R.TWTRACD.VLF.SS..D...PAVGL.T.EGR..LYWKT.R
Retrocopy LRELRARVRVLCWVVTCPQNVESRARHQRDTWTRACDRVLFLSSVDDAEFPAVGLGTEEGRQHLYWKTTR

Parental  AFQYVHEHHLGDADWFLKADDDTYVIVDNLRLMLSNYTPEQPIYFGRRFKPFVKQGYMSGGAGYVLSKEA
          A..Y..EHH..DADWFLKADDDTYV.VDNLRL.LS......P.YFGRRFK.......MSGGAGYVLS..A
Retrocopy AILYLREHHVDDADWFLKADDDTYVLVDNLRLLLSGHSARSPVYFGRRFKDRHNRSFMSGGAGYVLSRAA

Parental  LVRFVDAFAKGKCTHTSSVEDLAIGSCLEKIGVAAGDSRDSAARDTFHPFVPEHHLIANYLPKSFWYWKY
          LV...D.F..G.C...S..ED.AIG.CLEK.GVA.GDSRDSA.R.TFHPFVPE..L.........WYW.Y
Retrocopy LVLAADGFGSGQCGQVSLAEDVAIGACLEKVGVAFGDSRDSAGRETFHPFVPEKLLVRDFISNNSWYWRY

Parental  CFYPAVEGPQCCSDFTISFHYVSPTWMYILEYFAYHLRPYG
          C...AV.GPQCCSD...SFHYV.P..M..LEY....LRPYG
Retrocopy CYHRAVRGPQCCSDYPVSFHYVRPSYMHVLEYLVHRLRPYG

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_2 retrocopy.

TSS

Petromyzon marinus was not studied using FANTOM5 data.

Lab

retro_pmar_2 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000225	2 retrocopies	retro_chof_1782, retro_chof_2581,
Dasypus novemcinctus	ENSDNOG00000017353	2 retrocopies	retro_dnov_1801, retro_dnov_1905,
Homo sapiens	ENSG00000106392	2 retrocopies	retro_hsap_3177, retro_hsap_4065,
Loxodonta africana	ENSLAFG00000000063	1 retrocopy	retro_lafr_1166,
Myotis lucifugus	ENSMLUG00000014789	1 retrocopy	retro_mluc_1310,
Macaca mulatta	ENSMMUG00000016338	1 retrocopy	retro_mmul_2009,
Oryctolagus cuniculus	ENSOCUG00000026002	1 retrocopy	retro_ocun_216,
Otolemur garnettii	ENSOGAG00000012847	1 retrocopy	retro_ogar_855,
Petromyzon marinus	ENSPMAG00000001562	1 retrocopy	retro_pmar_2 ,
Pan troglodytes	ENSPTRG00000018925	2 retrocopies	retro_ptro_2266, retro_ptro_2755,