RetrogeneDB ID: retro_pmar_5

Retrocopy location

• Organism: Lamprey (Petromyzon marinus)
• Coordinates: GL482736:15658..16189(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPMAG00000010091
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPMAG00000000531
• Aliases: None
• Description: None

Sequence

>retro_pmar_5
ACAATGGGGAAATTCCTCTCCAAGATGTTCGGCAACAAGGAGATGCGCATTCTCATGCTGGGCCTGGACGCTGCCGGCAA
GACCACGATCCTGTACAAGCTCAAGCTCGGCCAGCCCGTCACCACCATTCCTACGGTGGGCTTCAACGTGGAGACTGTCA
CCTACAAGAACGTGCGCTTCAACGTGTGGGACGTGGGCGGCCAGGACAAGATCAGGCCCCTCTGGCGACACTACTACACG
GGCACGCAGGGACTCATCTTCGTGGTGGACTGCGCCGACCGAGACCGCGTGGACGAGGCTCGGCAGGAGCTGCACCGCAT
CATCAACGACCGCGAGATGCGCGATGCCATCATCCTGGTGTTCGCCAACAAGCAGGACCTGACCGACGCCATGAGGCCCC
ACGAGGTGCAGGAGAAGCTCGGACTGACCAGGGTCCGTGACCGCAACTGGTACGTGCAGCCGGCGTGCGCCTCCACTGGC
GACGGTCTCTACGAGGGCCTCACGTGGCTCACGTCCAACTACAAGTCGTAG

Alignment

ORF - retro_pmar_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.04 %
• Parental protein coverage: 98.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGGFFTRLFDTLVGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGG
          MG.F....F....G.KEMRILM.GLDAAGKTTILYKLKLG..VTTIPT.GFNVETV.YKN..F.VWDVGG
Retrocopy MGKFLSKMF----GNKEMRILMLGLDAAGKTTILYKLKLGQPVTTIPTVGFNVETVTYKNVRFNVWDVGG

Parental  QDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRNAVLLVFANKQDLPNAMNAAEIT
          QDKIRPLWRHY...TQGLIFVVD..DR.RV.EAR.EL.R.....E.R.A..LVFANKQDL..AM...E..
Retrocopy QDKIRPLWRHYYTGTQGLIFVVDCADRDRVDEARQELHRIINDREMRDAIILVFANKQDLTDAMRPHEVQ

Parental  DKLGLHSLRQRNWYIQATCATSGDGLYEGLDWLSNQLKN
          .KLGL...R.RNWY.Q..CA..GDGLYEGL.WL....K.
Retrocopy EKLGLTRVRDRNWYVQPACASTGDGLYEGLTWLTSNYKS

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_5 retrocopy.

TSS

Petromyzon marinus was not studied using FANTOM5 data.

Lab

retro_pmar_5 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 27 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008240	1 retrocopy	retro_acar_12,
Ailuropoda melanoleuca	ENSAMEG00000007042	2 retrocopies	retro_amel_28, retro_amel_70,
Canis familiaris	ENSCAFG00000008767	1 retrocopy	retro_cfam_119,
Cavia porcellus	ENSCPOG00000025074	1 retrocopy	retro_cpor_92,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Felis catus	ENSFCAG00000000088	2 retrocopies	retro_fcat_2, retro_fcat_59,
Homo sapiens	ENSG00000134287	1 retrocopy	retro_hsap_36,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Loxodonta africana	ENSLAFG00000004207	1 retrocopy	retro_lafr_115,
Macropus eugenii	ENSMEUG00000005072	7 retrocopies	retro_meug_1036, retro_meug_1117, retro_meug_1857, retro_meug_29, retro_meug_395, retro_meug_616, retro_meug_946,
Microcebus murinus	ENSMICG00000017545	1 retrocopy	retro_mmur_37,
Myotis lucifugus	ENSMLUG00000029846	1 retrocopy	retro_mluc_119,
Macaca mulatta	ENSMMUG00000006968	1 retrocopy	retro_mmul_174,
Monodelphis domestica	ENSMODG00000013804	1 retrocopy	retro_mdom_241,
Mustela putorius furo	ENSMPUG00000014730	1 retrocopy	retro_mputfur_86,
Mus musculus	ENSMUSG00000051853	1 retrocopy	retro_mmus_147,
Nomascus leucogenys	ENSNLEG00000017859	2 retrocopies	retro_nleu_1348, retro_nleu_94,
Ochotona princeps	ENSOPRG00000007411	2 retrocopies	retro_opri_13, retro_opri_3,
Petromyzon marinus	ENSPMAG00000000531	1 retrocopy	retro_pmar_5 ,
Pongo abelii	ENSPPYG00000004473	1 retrocopy	retro_pabe_126,
Pteropus vampyrus	ENSPVAG00000004626	1 retrocopy	retro_pvam_7,
Rattus norvegicus	ENSRNOG00000033155	1 retrocopy	retro_rnor_272,
Rattus norvegicus	ENSRNOG00000048089	1 retrocopy	retro_rnor_2521,
Sarcophilus harrisii	ENSSHAG00000003635	2 retrocopies	retro_shar_25, retro_shar_364,
Ictidomys tridecemlineatus	ENSSTOG00000004295	1 retrocopy	retro_itri_175,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000004698	1 retrocopy	retro_ttru_1081,