RetrogeneDB ID: retro_pmar_25

Retrocopy location

• Organism: Lamprey (Petromyzon marinus)
• Coordinates: GL497315:2667..3138(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: rab11bb
• Ensembl ID: ENSPMAG00000009335
• Aliases: None
• Description: RAB11B, member RAS oncogene family, b [Source:ZFIN;Acc:ZDB-GENE-040718-293]

Sequence

>retro_pmar_25
GTGGTTATGATAGGGGATTCTGGGGTTGGTAAATCTAATCTGTTGATGAGATATACCAAGGGAGATTTCAATATTGAATC
TAAAACTACAATTGGTGTTGAATTCGCGACAAAATCAATTAAAACTTAGGATAAGAAAGTAGTTAAAGCATAGATATGGG
ATACTGCTGGATAGGAACGCTACAGAGCTATAACAAACGCATATTACAGAGGAGCGGTCGGAGCATTACTTGTTTATGAT
GTCACTTGTATGGATAGTTTCCAGCACGTTAGTAACTGGTTGAAAGAATTGAAGTAATACGCAGACAGTAATATCGTGAT
TCTTCTTGTGGGAAATAAGACAGATTTAAAAGATAAACGTGAAGTAAGAAAAGAAGAAGCAGCAGCTTATGCCGATCAAC
ACAGTTTGGCTTTCATTGAGACCTCTGCACTGGACTGTTCTAATGTGGATTTGGCATTCGATCGTATCATT

Alignment

ORF - retro_pmar_25 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.97 %
• Parental protein coverage: 75.36 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQV-DGKTIKAQIWDTAGQERYRAITSAYYR
          VV.IGDSGVGKSNLL.R.T...FN.ESK.TIGVEFAT.SI...D.K..KA.IWDTAG.ERYRAIT.AYYR
Retrocopy VVMIGDSGVGKSNLLMRYTKGDFNIESKTTIGVEFATKSIKT*DKKVVKA*IWDTAG*ERYRAITNAYYR

Parental  GAYGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVTTDEAKAFAENHGLSFIE
          GA.GALLVYD.........V..WLKEL...ADSNIVI.LVGNK.DL...R.V...EA.A.A..H.L.FIE
Retrocopy GAVGALLVYDVTCMDSFQHVSNWLKELK*YADSNIVILLVGNKTDLKDKREVRKEEAAAYADQHSLAFIE

Parental  TSALDSTNVESAFITIL
          TSALD..NV..AF..I.
Retrocopy TSALDCSNVDLAFDRII

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_25 retrocopy.

TSS

Petromyzon marinus was not studied using FANTOM5 data.

Lab

retro_pmar_25 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 20 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018959	1 retrocopy	retro_btau_1850,
Choloepus hoffmanni	ENSCHOG00000013525	1 retrocopy	retro_chof_1582,
Callithrix jacchus	ENSCJAG00000007333	1 retrocopy	retro_cjac_1050,
Callithrix jacchus	ENSCJAG00000010778	2 retrocopies	retro_cjac_3866, retro_cjac_3917,
Erinaceus europaeus	ENSEEUG00000009165	2 retrocopies	retro_eeur_284, retro_eeur_565,
Echinops telfairi	ENSETEG00000004920	5 retrocopies	retro_etel_1150, retro_etel_2132, retro_etel_2214, retro_etel_694, retro_etel_837,
Homo sapiens	ENSG00000103769	1 retrocopy	retro_hsap_715,
Gorilla gorilla	ENSGGOG00000014252	2 retrocopies	retro_ggor_538, retro_ggor_605,
Myotis lucifugus	ENSMLUG00000008820	2 retrocopies	retro_mluc_1606, retro_mluc_2435,
Macaca mulatta	ENSMMUG00000008006	1 retrocopy	retro_mmul_2463,
Mus musculus	ENSMUSG00000077450	1 retrocopy	retro_mmus_1846,
Nomascus leucogenys	ENSNLEG00000012853	1 retrocopy	retro_nleu_467,
Otolemur garnettii	ENSOGAG00000003227	1 retrocopy	retro_ogar_2405,
Petromyzon marinus	ENSPMAG00000009335	1 retrocopy	retro_pmar_25 ,
Pongo abelii	ENSPPYG00000006573	1 retrocopy	retro_pabe_618,
Pan troglodytes	ENSPTRG00000007188	1 retrocopy	retro_ptro_510,
Pteropus vampyrus	ENSPVAG00000009645	1 retrocopy	retro_pvam_64,
Sarcophilus harrisii	ENSSHAG00000006816	1 retrocopy	retro_shar_189,
Tupaia belangeri	ENSTBEG00000000667	1 retrocopy	retro_tbel_4634,
Tarsius syrichta	ENSTSYG00000014758	1 retrocopy	retro_tsyr_802,