RetrogeneDB ID: retro_pmar_7

Retrocopy location

• Organism: Lamprey (Petromyzon marinus)
• Coordinates: GL499136:453..1347(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPMAG00000010258
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPMAG00000003453
• Aliases: None
• Description: None

Sequence

>retro_pmar_7
AAGACCTACGACCAGAATGAGGAGGGCTGGAGGAGGATGATTTGGGAGAAGAACCTCAAGAAGATCGCGGTGCACAACCT
GGAGCACTCCATGGGCAAGCACACCTGGCGCATGGGCATGAACCGCTTCGGTGACATGACAAAAGAGGAGTTCCAGCATA
CCATGCTGGGCCTCAGGGGCTCGAATGACACCAGCAAGGCCTCCCGCGGTGCCACATTCATGGCGCCCGCCTTCTTCAAG
GCTCCCGAGTCCGTCGACTGGAGGAAGCAAGGCTACGTCACCGACGTCAAGGACCAGGGCGACTGCGGCTCTTGCTGGGC
GTTCAGCACCACGGGTTCCCTCGAGGGACAGCACAAGCGCAAGACTGGAGTGCTCGTGTCGCTGAGCGAGCAGAACCTGG
TGGACTGCTCTTCTGCCGAGGGCAATAACGGCTGCAAGGGAGGACTCATGGACTTGGCATTTACCTACATCAAGAAGAAT
GGTGGTATCGACTCTGAGGCGTCGTACCCGTACACGGCAAAGGATGAGAATTGCAAATACAACCCCAAGAACAAGGCCGC
CGAGGACACCGGCTTCGTGGACATCCCCAGCGGGAATGAGGAGGCCCTCAAGAACGCCGTGGCTTCCGTTGGCCCGGTGT
CGATCGGCATTGACGCCAGCCTCGAATCCTTCCAGTTGTACAGCTCCGGCATTTACAGTGACAGCGATTGCTCCAACAAC
CTTGATCATGGCGTGTTGGTTGTGGGCTATGGTGTGGATGATGACGAACGTAAATTCTGGATTGTCAAGAACAGCTGGGG
AACGAAGTGGGGAGATCATGGATACATCCTTATGGCACGTGATAAGGATAACCTGTGTGGCATTGCCACTGCTGCAAGCT
ATCCCCTGGTGTAA

Alignment

ORF - retro_pmar_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.27 %
• Parental protein coverage: 99.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QNEEGWRRMIWEQNLKKIAVHNLEHSMGKHTWRMGMNRFGDMTGEEFQQVMLGFRGWNGTSKAPRGATFM
          QNEEGWRRMIWE.NLKKIAVHNLEHSMGKHTWRMGMNRFGDMT.EEFQ..MLG.RG.N.TSKA.RGATFM
Retrocopy QNEEGWRRMIWEKNLKKIAVHNLEHSMGKHTWRMGMNRFGDMTKEEFQHTMLGLRGSNDTSKASRGATFM

Parental  APAFFEAPESVDWRKQGYVTDVKNQGDCGSCWSFSTTGSLEGQHKRKTGVLVSLSEQNLVDCSSTEGNYG
          APAFF.APESVDWRKQGYVTDVK.QGDCGSCW.FSTTGSLEGQHKRKTGVLVSLSEQNLVDCSS.EGN.G
Retrocopy APAFFKAPESVDWRKQGYVTDVKDQGDCGSCWAFSTTGSLEGQHKRKTGVLVSLSEQNLVDCSSAEGNNG

Parental  CNGGLMINAFNYIKKNGGIDSEESYPYKGQGVETCKYNPKNKAAEVTGYVEIPEGDEEALKNAVASVGPV
          C.GGLM..AF.YIKKNGGIDSE.SYPY.....E.CKYNPKNKAAE.TG.V.IP.G.EEALKNAVASVGPV
Retrocopy CKGGLMDLAFTYIKKNGGIDSEASYPYTAKD-ENCKYNPKNKAAEDTGFVDIPSGNEEALKNAVASVGPV

Parental  SVAIDASLNSFLYYISGIYKDKLCSHIINHAVLVVGYGVDEKGDKFWLVKNSWGVQWGEKGYVRMARDDN
          S..IDASL.SF..Y.SGIY.D..CS....H.VLVVGYGVD....KFW.VKNSWG..WG..GY..MARD..
Retrocopy SIGIDASLESFQLYSSGIYSDSDCSNNLDHGVLVVGYGVDDDERKFWIVKNSWGTKWGDHGYILMARDKD

Parental  NLCGIAVTASYPLV
          NLCGIA..ASYPLV
Retrocopy NLCGIATAASYPLV

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_7 retrocopy.

TSS

Petromyzon marinus was not studied using FANTOM5 data.

Lab

retro_pmar_7 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 18 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001149	1 retrocopy	retro_cfam_43,
Choloepus hoffmanni	ENSCHOG00000007548	8 retrocopies	retro_chof_1227, retro_chof_1332, retro_chof_1345, retro_chof_141, retro_chof_1464, retro_chof_2392, retro_chof_383, retro_chof_424,
Dasypus novemcinctus	ENSDNOG00000012037	1 retrocopy	retro_dnov_2387,
Dipodomys ordii	ENSDORG00000019810	1 retrocopy	retro_dord_197,
Echinops telfairi	ENSETEG00000007977	1 retrocopy	retro_etel_1465,
Macropus eugenii	ENSMEUG00000002168	2 retrocopies	retro_meug_1349, retro_meug_1567,
Macropus eugenii	ENSMEUG00000014293	1 retrocopy	retro_meug_1873,
Macropus eugenii	ENSMEUG00000016209	2 retrocopies	retro_meug_159, retro_meug_1727,
Myotis lucifugus	ENSMLUG00000003975	1 retrocopy	retro_mluc_2231,
Myotis lucifugus	ENSMLUG00000025440	1 retrocopy	retro_mluc_2399,
Macaca mulatta	ENSMMUG00000013861	1 retrocopy	retro_mmul_1669,
Monodelphis domestica	ENSMODG00000002844	1 retrocopy	retro_mdom_1101,
Otolemur garnettii	ENSOGAG00000001349	2 retrocopies	retro_ogar_1053, retro_ogar_1373,
Ochotona princeps	ENSOPRG00000001030	2 retrocopies	retro_opri_186, retro_opri_499,
Petromyzon marinus	ENSPMAG00000003453	1 retrocopy	retro_pmar_7 ,
Tupaia belangeri	ENSTBEG00000016406	1 retrocopy	retro_tbel_2841,
Tarsius syrichta	ENSTSYG00000002858	2 retrocopies	retro_tsyr_150, retro_tsyr_603,
Vicugna pacos	ENSVPAG00000004397	1 retrocopy	retro_vpac_433,