RetrogeneDB ID: retro_ttru_1560

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_116322:91867..92653(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNMT
• Ensembl ID: ENSTTRG00000012879
• Aliases: None
• Description: histamine N-methyltransferase [Source:HGNC Symbol;Acc:5028]

Sequence

>retro_ttru_1560
TGCATGCAGCAATTCATGGACGAGAAGCTGCCGGGCATAATAGCAAGGATTGGAGACACAAAATCTGAAATTAAGACTCT
AAGCATTGGTGGAGGTGCAGGTGAAACTGATCTTCATATCCTCTCCAAAGTGCAGGCTCAATACCCTGGAGTTAGTATCA
ACAATGAAGTTGTTGAACCAAGTGCTGAACAAATCACCAAGTACAAAGAGCTTGTAGCCAAGACATCAAACCTCGAGAAC
ATAAAGTTTACTTGGCATAAGGAGGCATCACCTGAATATCAAAATAGAATGATGGAGAAAAAAGAACTTCAGAAGTGGGA
CTTTATTCATATGATTCAGATGCTGTATTATGTAAAAGACATCCCAGCCACCCTGAAATTCTTCCATAGTCTCTTAGCTA
CCAGTGCTAAGATTCTCATTACTCTTGTGTCCAGAACCAGTGGCTGGGACAAGCTATGGAAAAAGTACAGATCTCACTTA
CCCCGGGATGACCTCTGCCAGTATGTCACGTCATCTGACCTCGTGCAGATGCTGGACAAGTTGGGGATTAAGTATGAGTG
TTATGACCTTCTGTCCACCATGGACATATCTGACTGTTTTAATGACAGCAATGAAAATGAAGACCTGCTTTGGGATTTTT
TGACAGAAACCTGCAACTTTAGTACAACAGCACCACCTGATCTCAAAGCAGAAATTATGAAAGATCTGCAAGACCCTGAA
TTCAGTGTAAAGAAAGAGGGAAAGGTTCTTTTCAATAACAGTCTGAGTTTCATAGTGGTTGAGGCA

Alignment

ORF - retro_ttru_1560 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.75 %
• Parental protein coverage: 89.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CMQQFMDEKLPGIIARIGDTKSEIKILSIGGGAGEIDLHILSKVQAQYPGVSINTEVVEPSTEQISKYKE
          CMQQFMDEKLPGIIARIGDTKSEIK.LSIGGGAGE.DLHILSKVQAQYPGVSIN.EVVEPS.EQI.KYKE
Retrocopy CMQQFMDEKLPGIIARIGDTKSEIKTLSIGGGAGETDLHILSKVQAQYPGVSINNEVVEPSAEQITKYKE

Parental  LVAKTSNLENIKFTWHKETSSEYQNRMMEKKELQKWDFIHMIQMLYYVKDIPGTLKFFHSLLATGAKILI
          LVAKTSNLENIKFTWHKE.S.EYQNRMMEKKELQKWDFIHMIQMLYYVKDIP.TLKFFHSLLAT.AKILI
Retrocopy LVAKTSNLENIKFTWHKEASPEYQNRMMEKKELQKWDFIHMIQMLYYVKDIPATLKFFHSLLATSAKILI

Parental  TLVSGTSGWDKLWKKYGSHLPRDDLCQCVTSSDLMQMLDKLGIKYECYDLLSTMDISDCFIDGNENGDLL
          TLVS.TSGWDKLWKKY.SHLPRDDLCQ.VTSSDL.QMLDKLGIKYECYDLLSTMDISDCF.D.NEN.DLL
Retrocopy TLVSRTSGWDKLWKKYRSHLPRDDLCQYVTSSDLVQMLDKLGIKYECYDLLSTMDISDCFNDSNENEDLL

Parental  WDFLTETWNFSTTAPPDLKAEIMKDLQEPEFSVKKEGKVLFNNSLSFIVAEA
          WDFLTET.NFSTTAPPDLKAEIMKDLQ.PEFSVKKEGKVLFNNSLSFIV.EA
Retrocopy WDFLTETCNFSTTAPPDLKAEIMKDLQDPEFSVKKEGKVLFNNSLSFIVVEA

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1560 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1560 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015340	1 retrocopy	retro_dnov_1969,
Myotis lucifugus	ENSMLUG00000015156	2 retrocopies	retro_mluc_1174, retro_mluc_1417,
Monodelphis domestica	ENSMODG00000001168	1 retrocopy	retro_mdom_932,
Tursiops truncatus	ENSTTRG00000012879	1 retrocopy	retro_ttru_1560 ,