RetrogeneDB ID: retro_gmor_2

Retrocopy location

• Organism: Cod (Gadus morhua)
• Coordinates: GeneScaffold_1631:106760..108317(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGMOG00000019740
• 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_2
GTGGTTCTCCCCATGGCGCTGGCCCTCCTGTCTGCTGCTAGTGTCCAAGGTGGTAAAGTCCTGGTGTTCCCAGTGGACGG
CAGCCATTGGATCAACATGAACCTGCTGATCGAGGGTCTCCACGGCAGGGGTCACGAGGTCACGGTGGTCCGCACGTCAA
CAAGCTGGTACATCAAGGAGCAGTCCCCCCACTACACCTCCATCACCATCTCCCTGTCTGAAGCCATGAACCTGGAAAAC
CAGGACTTCTTCGTGGAGTTCCTGTCCAAGATGCTGGCCCTCCAGAAAGAGGGAGCGTCCGTGTTGGCCTTTGTCTCCTT
CTACAGCCAGATGCTGACAACGCTGTCCGGTATTCACCACCAGGCTTGCCAGGTCGCCGTGAAGATGTTCGAAGACAAGG
CGTTGATGCAGAGCCTGCGAGACGCCCAGTATGACGTGGTCCTGATGGATCCAGGTCTGCCCATCGGGGTTCTCTTGGCT
CATGAGCTCAAACTCCCCACAGTTTTTAACGTTCGGTGGATCACCAGCGGAGAGGGACACTTTGTGGTCGCGCCCTCCCC
CGTTTCTTACGTTCCCACTAGCGGTTGTGCAGTGACGGACAAGATGACCTTCCCGGAGAGGGTCAAAAACATGTTCCATT
TCATGCTGAACATAGTCATCGATAAAATGGTGGTGAGCCCTCACTACAATCGACTGGCCGAGAAGTATCTAGAACCTGGG
ACCAATTTCTACCAACTCCTACAGGGAGCGCACATCTGGCTCATGAGGGTGGACTTTGTCTTTGAGTTCCCCAGACCTAC
CATGCCAAACATCATCTACGTTGGCGGCTTCCAGTGTAAACCCTCAAAGCCTCTGCCTGCTGATCTGGAGGACTTCGTCC
AGAGCTCAGGGGAACACGGTGTGATCGTGATGTCACTGGGTTCCCTGGTCAAAGGCCTGCCCGTTGAGATCACCAACCAG
ATTGCCACTGCCTTCGCACAGCTTCCCCAGAAGGTCATCTGGAGGCTCCCCGGAGAGCCGCCGAGCACCTTGGGAAACAA
CACCATGCTGGTGAAATGGTTGCCTCAGAACGACCTTCTCGGCCACCCCAAGGTCAAAGCGTTTGTCGCCCACGGGGGGA
CCAACGGCATCTATGAGGCCATATACCACAAGGTGCCCATCGTGGGCATACCCCTGCTCTTCGACCAGTTTGAGAACATC
TTGAGGCTGGAAGTGCGCGGTGCTGCTAAGGGAGTGGACGTCACCAAACTCACCAGCCAGAACTTTGTCGAAACACTACA
AGAGGTTCTACATGATCCTTCCTACAGGGACAGCATGAAGCGGTTGTCGGACCTCCACCGGGACAAGCCCATGCACCCTC
TGGACACTGCCCTCTTTTGGGTAGAGTTTGTAATGCGGAACAAGGGAGCCGCCCACTTGCGTACTGAGTCCTATAAATTG
CCTTGGTACTCGTATCATTCATTGGACGTTATGTGCCTGCTGGTGGCTGTGCTGTCCCTGTTGGTAGCAGTCATAGTTCT
CTCAATTTATTATATTTGTTCTAAACTGTGCAGGAGA

Alignment

ORF - retro_gmor_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.4 %
• Parental protein coverage: 95.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IPLLFTAPSDGGKVLVYPVDGSHWINMKIVIEELHARGHSIDVIRASDSWYIREESPLYSSITIPVDTPM
          ..LL..A...GGKVLV.PVDGSHWINM...IE.LH.RGH...V.R.S.SWYI.E.SP.Y.SITI.....M
Retrocopy LALLSAASVQGGKVLVFPVDGSHWINMNLLIEGLHGRGHEVTVVRTSTSWYIKEQSPHYTSITISLSEAM

Parental  ----ENFFLIYLEKYMKAQRERASVFTFLKLTSQFMSMISKAHSVNCDMLGQILDDESLVQRLSDAQYDL
          ......FF...L.K....Q.E.ASV..F....SQ.....S..H...C........D..L.Q.L.DAQYD.
Retrocopy NLENQDFFVEFLSKMLALQKEGASVLAFVSFYSQMLTTLSGIHHQACQVAVKMFEDKALMQSLRDAQYDV

Parental  VLTDPAIATGVVLAKYLKLPLVLNVRWITSGDGQFAIAPSPLSYVPVPGSGLTDKMSFTERTQNMLFHSL
          VL.DP....GV.LA..LKLP.V.NVRWITSG.G.F..APSP.SYVP..G...TDKM.F.ER..NM....L
Retrocopy VLMDPGLPIGVLLAHELKLPTVFNVRWITSGEGHFVVAPSPVSYVPTSGCAVTDKMTFPERVKNMFHFML

Parental  IVFQERFMVGPSYHAICDKYIEGGCDIISLIQEADIWLFRSDFVFDFPRPTMPNVVYIGGFQCKPAQPLP
          ........V.P.Y.....KY.E.G.....L.Q.A.IWL.R.DFVF.FPRPTMPN..Y.GGFQCKP..PLP
Retrocopy NIVIDKMVVSPHYNRLAEKYLEPGTNFYQLLQGAHIWLMRVDFVFEFPRPTMPNIIYVGGFQCKPSKPLP

Parental  SGLEEFVQSAGEHGVIIMTLGTLVNALPDDIAEEIASVFARMPQKVIWRNIGKRPSTLGNNTLIVDWMPQ
          ..LE.FVQS.GEHGVI.M.LG.LV..LP..I...IA..FA..PQKVIWR..G..PSTLGNNT..V.W.PQ
Retrocopy ADLEDFVQSSGEHGVIVMSLGSLVKGLPVEITNQIATAFAQLPQKVIWRLPGEPPSTLGNNTMLVKWLPQ

Parental  KDLLGHPQTKVFVAHGGTNGVQEAIYYGVPVLGIPLFFDQYDNLLRLQERGAGKILKLAEVNGRTFEQGL
          .DLLGHP..K.FVAHGGTNG..EAIY..VP..GIPL.FDQ..N.LRL..RGA.K...........F...L
Retrocopy NDLLGHPKVKAFVAHGGTNGIYEAIYHKVPIVGIPLLFDQFENILRLEVRGAAKGVDVTKLTSQNFVETL

Parental  GEVLHQDSYRNNMQRLSRLHRDQPIPPLEHAIFWTEYVMRHKGAPHLRTESYRMPWYSYYSIDVMMTLLA
          .EVLH..SYR..M.RLS.LHRD.P..PL..A.FW.E.VMR.KGA.HLRTESY..PWYSY.S.DVM..L.A
Retrocopy QEVLHDPSYRDSMKRLSDLHRDKPMHPLDTALFWVEFVMRNKGAAHLRTESYKLPWYSYHSLDVMCLLVA

Parental  AVTIFLLSIVIMFRFLCCRVC
          ........IV......C...C
Retrocopy VLSLLVAVIVLSIYYICSKLC

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_2 retrocopy.

TSS

Gadus morhua was not studied using FANTOM5 data.

Lab

retro_gmor_2 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,