RetrogeneDB ID: retro_gmor_3

Retrocopy location

• Organism: Cod (Gadus morhua)
• Coordinates: GeneScaffold_4464:81355..82906(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGMOG00000020354
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ugt5d1 (1 of 2)
• Ensembl ID: ENSGMOG00000010454
• Aliases: None
• Description: UDP glucuronosyltransferase 5 family, polypeptide D1 [Source:ZFIN;Acc:ZDB-GENE-091118-36]

Sequence

>retro_gmor_3
GTGCTACTCGCCGCGTTGTTCTGCTACGTGGGCCCCGTCGACGGTGGTAAGGTCCTGGTTGTCCCGGTTGATGGGAGCCA
CTGGATCAACATGAAGGTGCTGATGGAGGAGCTGCACTCCAGAGGTCATGAAATCACAGTGCTGCGGCCCAACGACGCCT
GGTACATCAAGGACAACTCTCCTTACTACCGCACTGTCACAGTCGACTTCTCCGCTGGCTTCAACGAGGAGGACTTTGGT
TCAATGGCTGCCCGCATCATCAGCCTGCGGCGTGCTGGGGGGTCCGTATGGCACCGCATGTCCGTGGAGATGGAGATGTT
ATTCATGTTCCGGCAGTTTCACTTGTCAACCGTCAACATGATTGAGAAAATCTTTGAAGACGGGGAGCTGATGCAGAGCT
TCCAAAAGGCCGGGTACGACCTGGTTCTGACAGACCCGGCCATGGGGACGGGCGTGCTGCTGGCCCGACGTCTGGGTCTC
CCTCTGGTCCTCAATGTCAGGTGGACCATCCAGGGGGAGGGCCATGGAGCAATATGCCCAAGCCCCCTCTCCTATGTTCC
CACCCCAGGGGCAGAGCTGACGGACGTGATGAGCTTCACCCAGCGGATCAGCAACACCCTCTTCTATCTATTCACCCGGC
TACAGATCGCCTTCATCATTGAACCGAACTATGGGCCCCTGGTGCAGCGCTACTTCGGCGTGCACTACATGGAGCTGTTC
CAGGCCGCAGACATCTGGTTGATGAGGACCGACTTCACCTTTGAGTTCCCTCGGCCCACCATGCCCAACATCGTCTACAT
GGCCGGCTTCCAGTGCAAGCCCTCCAAGCCCCTCTCCCCAGACCTGGAGGCCTTTGTCCAGAGTGCGGGGGAGCACGGCG
TCATCATCATGACCCTGGGGACGCTGGTGGGAGGGCTGCCTGAGGAACTGACGGAGGACATCGCTGCAGCGTTCGCTGAG
TTGCCCCAGAAGGTGGTGTGGCGGCACACCGGCAAAAGGCCCTCCACCGTGGGGAACAACACCTTGCTGCTAGACTGGCT
GCCCCAGAATGACCTCCTCGGCCACCCCAGCACCAGACTTTTTGTGGCACACGGTGGGACCAATGGCATCCAGGAGGCTA
TCTACCACGGGGTGCCTCTGGTGGGCCTGCCGCTGATGTTCGACCAGCTGGACAACTTCTCCAGGGTGAGAGCCAGAGGC
GTGGCCAAGGTCCTCGACCTCTCCACGGTGAACAGAGAAAGCTTCCTGTCGGCCCTGAAGGAGGTGCTCTACCAGCCCAC
CTACCGGGACAAGATGCAGCGTCTGTCTGCGCTGCACAGAGACCAGCCCACCAAGCCCCTGGAGAGAGCCATGTTCTGGA
TAGAGTTTGTGATGAGACACAAGGGGGCGCCACACCTCAGAACGGACTCCTACAAGATGTCAACAGTTCAGTACTACAGT
GTGGATGTGGCCCTGTTCCTCCTGTCGGTTGTGCTGCTGGTCCTGCTTATCTCCGGTGCTACACTTAGGTTCTTATGGCG
CCGGGTGGTGCGCAGGAGTAAAGGCAAGCAG

Alignment

ORF - retro_gmor_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.12 %
• Parental protein coverage: 95.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FTAPSDGGKVLVYPVDGSHWINMKIVIEELHARGHSIDVIRASDSWYIREESPLYSSITIPVDTPM-ENF
          ...P.DGGKVLV.PVDGSHWINMK...EELH.RGH.I.V.R..D.WYI...SP.Y...T........E..
Retrocopy YVGPVDGGKVLVVPVDGSHWINMKVLMEELHSRGHEITVLRPNDAWYIKDNSPYYRTVTVDFSAGFNEED

Parental  FLIYLEKYMKAQRERASVFTFLKLTSQFMSMISKAHSVNCDMLGQILDDESLVQRLSDAQYDLVLTDPAI
          F...........R...SV............M....H.....M...I..D..L.Q....A.YDLVLTDPA.
Retrocopy FGSMAARIISLRRAGGSVWHRMSVEMEMLFMFRQFHLSTVNMIEKIFEDGELMQSFQKAGYDLVLTDPAM

Parental  ATGVVLAKYLKLPLVLNVRWITSGDGQFAIAPSPLSYVPVPGSGLTDKMSFTERTQNMLFHSLIVFQERF
          .TGV.LA..L.LPLVLNVRW...G.G..AI.PSPLSYVP.PG..LTD.MSFT.R..N.LF......Q..F
Retrocopy GTGVLLARRLGLPLVLNVRWTIQGEGHGAICPSPLSYVPTPGAELTDVMSFTQRISNTLFYLFTRLQIAF

Parental  MVGPSYHAICDKYIEGGCDIISLIQEADIWLFRSDFVFDFPRPTMPNVVYIGGFQCKPAQPLPSGLEEFV
          ...P.Y......Y...G.....L.Q.ADIWL.R.DF.F.FPRPTMPN.VY..GFQCKP..PL...LE.FV
Retrocopy IIEPNYGPLVQRYF--GVHYMELFQAADIWLMRTDFTFEFPRPTMPNIVYMAGFQCKPSKPLSPDLEAFV

Parental  QSAGEHGVIIMTLGTLVNALPDDIAEEIASVFARMPQKVIWRNIGKRPSTLGNNTLIVDWMPQKDLLGHP
          QSAGEHGVIIMTLGTLV..LP....E.IA..FA..PQKV.WR..GKRPST.GNNTL..DW.PQ.DLLGHP
Retrocopy QSAGEHGVIIMTLGTLVGGLPEELTEDIAAAFAELPQKVVWRHTGKRPSTVGNNTLLLDWLPQNDLLGHP

Parental  QTKVFVAHGGTNGVQEAIYYGVPVLGIPLFFDQYDNLLRLQERGAGKILKLAEVNGRTFEQGLGEVLHQD
          .T..FVAHGGTNG.QEAIY.GVP..G.PL.FDQ.DN..R...RG..K.L.L..VN...F...L.EVL.Q.
Retrocopy STRLFVAHGGTNGIQEAIYHGVPLVGLPLMFDQLDNFSRVRARGVAKVLDLSTVNRESFLSALKEVLYQP

Parental  SYRNNMQRLSRLHRDQPIPPLEHAIFWTEYVMRHKGAPHLRTESYRMPWYSYYSIDVMMTLLAAVTIFLL
          .YR..MQRLS.LHRDQP..PLE.A.FW.E.VMRHKGAPHLRT.SY.M....YYS.DV...LL..V...LL
Retrocopy TYRDKMQRLSALHRDQPTKPLERAMFWIEFVMRHKGAPHLRTDSYKMSTVQYYSVDVALFLLSVVLLVLL

Parental  SIVIMFRFLCCRGVLNNK
          ......RFL..R.V...K
Retrocopy ISGATLRFLWRRVVRRSK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Gadus morhua was not studied using RNA-Seq expression data.

ChIP-Seq

Gadus morhua was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_gmor_3 retrocopy.

TSS

Gadus morhua was not studied using FANTOM5 data.

Lab

retro_gmor_3 was not experimentally validated.

Homology

Retrocopy orthology:

Gadus morhua 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Gadus morhua	ENSGMOG00000010454	2 retrocopies	retro_gmor_2, retro_gmor_3 ,