RetrogeneDB ID: retro_pmar_8

Retrocopy location

• Organism: Lamprey (Petromyzon marinus)
• Coordinates: GL485859:2700..4509(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPMAG00000009982
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPMAG00000005873
• Aliases: None
• Description: None

Sequence

>retro_pmar_8
AGCGTCTCGTGTCGGGAGATGCTGTGCCAGAACATCACGGTGCCCATGTGCCGGGGCATCGGCTACAACCACACGTACAT
GCCCAACGACTTCAACCACGACTCGCAGGACGAGGCGGGCCTCGAGGTGCACCAGTTCTGGCCTCTCGTCGAGATCAAGT
GCTCGCCGGACCTTCGCTTCTTCCTGTGCAGCATGTACACTCCGATCTGCCTGGAGGACTACAAGCAGCCGCTGCCGCCG
TGCCGCTCGGTGTGCGAGAGGGCCCGCGCCGGCTGCGCGCCGCTCATGCGCCAGTACGGATTCGCGTGGCCCGACCGCAT
GCGCTGCGACCGCCTGCCAGTCCTGGGTGACCAGAACCGCCTGTGCATGGACTACAACAAGAGCGACACCACGCCGCAGC
CGCCCGAGGTGAAGCCCACGGCGCCGGTCAGGTCCTTCAACCCGAGCAAGAACAGGGCGACCACCAGAGTTGGTGGTGGT
GGTGGTGGCGGCGGTGGGAGCGGAGAGGCTTGCGAGTCCGGCTGCGCGTGTAGGGCCCCCATGGTGGCCATCGGCAGTGA
CAGGCACCCGCTGTACAACCGCGTGCGCACCGGCTCCGTGCTGAACTGCGCGATGCCGTGCCACGACCCTTACTTCACGC
AGGACGAGCGCACCTTCGCCTCCTTCTGGATCGGCCTGTGGTCCATCTTGTGCTTCGTGTCCACCTTCACCACGGTGGTC
ACCTTCCTCATCGACATGGAGCGCTTCAAGTACCCGGAGCGGCCCATCATCTTCCTGTCGGCGTGCTACGCCTTCGTGTC
CATGGGCTACATCGTGAGGTTGGTGGTGGGTCACGACGGGGTGATCTGCAACCAGGAGCACAGGCACGTCCACTACGAGA
CCACGGGCCCCGCGCTCTGCACCGTGGTATTCCTCCTCACCTACTTCTTCGGCATGGCCAGCTCCATCTGGTGGGTCATC
CTCTCCCTCACCTGGTTCATGGCTGCCGGCATGAAGTGGAGCAGCGAGGCCATCGCGGGCTACTCGCAGTACTACCACCT
GGCCGCGTGGCTCCTGCCCAGCGTGCAGTCGGTGGCCGTGCTGGCCACGAGCTCCGTGGACGCCGACCCTCTGGCCGGCA
TATGCTCGGTGGGCGCCCAGAGCCTGGAGAATCTGCGCGGCTTCGTCCTCGTGCCGCTCACCGTCTACCTGTGCGTGGGC
GCCGTCTTCCTGCTGGCCGGATTCACGTCGCTCGTGCGGATACGCAACGCCATCAAGCAGCAGGGCGGCACCAAGACGGA
CAAGCTGGAGAAGCTCATGGTGCGAATCGGCATCTTCAGCATGCTGTACACGGTGCCAGCGATCGCCGTGGTGGCCTGCT
ACTTCTACGAGGAGCGCTCCCGCGACGGCTGGGCCAGAGCCCTCATCTGCCCCTCGTGCCAAGGTGACGAGGAGCCGGGC
TCGCAGCAGCAGCAGCAGCAGCGACCCGACTACGGCATCTTCATGCTCAAGTATTTCATGTGCCTCGTGGTGGGCATCAC
CTCGGGCGTGTGGATATGGTCGGGCAAGACCGTGGACACGTGGAAAAGGCTCTGCTGCCGGTGCTGCGGTCTGGGTGGCA
AATCGTCGGGAGCCGCGGTATACAGCGAGGTGCACGGCGGCAGTGGTGGTGGAGGAGGAGGAGGAGGGCACCATCACCAT
CACCACCACCATCATCACCTGGGCACGGCGAGCGGTGGGCCCGGGACGGCTGTTGGGGCGGCGCGGGCCGCCAGCAGCGT
CGCGAGCTCCGTGTCCTGCCACAAGCCGGCGCCTCTGTCGCTCGTCTGA

Alignment

ORF - retro_pmar_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.02 %
• Parental protein coverage: 92.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CEPICGCRAPLVRISNPRHVLYDRVRTGQVRNCATPCHSPFLGREQRTFASFWIGLWSSLCFAATFATVS
          CE..C.CRAP.V.I...RH.LY.RVRTG.V.NCA.PCH.P......RTFASFWIGLWS.LCF..TF.TV.
Retrocopy CESGCACRAPMVAIGSDRHPLYNRVRTGSVLNCAMPCHDPYFTQDERTFASFWIGLWSILCFVSTFTTVV

Parental  TFLIDMERFKYPERPIIFLSLCCMLASLGYIVRMVAGHEAVACSADWHHVLYASSGPALCTAVFLLTYFF
          TFLIDMERFKYPERPIIFLS.C....S.GYIVR.V.GH..V.C.....HV.Y...GPALCT.VFLLTYFF
Retrocopy TFLIDMERFKYPERPIIFLSACYAFVSMGYIVRLVVGHDGVICNQEHRHVHYETTGPALCTVVFLLTYFF

Parental  GMAGCVWWVILSLTWFMAAGLKWGSEAIAGYSQYYHLAAWLLPSIKAIAALAMNAVDGDPVAGICSVGNQ
          GMA...WWVILSLTWFMAAG.KW.SEAIAGYSQYYHLAAWLLPS....A.LA...VD.DP.AGICSVG.Q
Retrocopy GMASSIWWVILSLTWFMAAGMKWSSEAIAGYSQYYHLAAWLLPSVQSVAVLATSSVDADPLAGICSVGAQ

Parental  SLDNLRGFVLAPLVAYLLVGTAFLLAGLVALFRIRNAISANPGGAKTEKLERLMVRIGVFAVLYTVPAAV
          SL.NLRGFVL.PL..YL.VG..FLLAG...L.RIRNAI....GG.KT.KLE.LMVRIG.F..LYTVPA..
Retrocopy SLENLRGFVLVPLTVYLCVGAVFLLAGFTSLVRIRNAIK-QQGGTKTDKLEKLMVRIGIFSMLYTVPAIA

Parental  AVVCHLYEQQHRDSWERTLVCGAC--GPGPGHLPEPGARPDFAVFMLKYFVCLVGGITSGAWIWSGKTAG
          .V.C..YE...RD.W.R.L.C..C.....PG.......RPD...FMLKYF.CLV.GITSG.WIWSGKT..
Retrocopy VVACYFYEERSRDGWARALICPSCQGDEEPGSQQQQQQRPDYGIFMLKYFMCLVVGITSGVWIWSGKTVD

Parental  SWKRFYKRC
          .WKR...RC
Retrocopy TWKRLCCRC

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_8 retrocopy.

TSS

Petromyzon marinus was not studied using FANTOM5 data.

Lab

retro_pmar_8 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001137	1 retrocopy	retro_acar_5,
Callithrix jacchus	ENSCJAG00000014119	1 retrocopy	retro_cjac_213,
Ficedula albicollis	ENSFALG00000007019	1 retrocopy	retro_falb_7,
Petromyzon marinus	ENSPMAG00000005873	1 retrocopy	retro_pmar_8 ,