RetrogeneDB ID: retro_ttru_489

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_246:389927..391010(-)
• Located in intron of: ENSTTRG00000014440

Retrocopy information

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

Parental gene information

• Parental gene symbol: BHMT2
• Ensembl ID: ENSTTRG00000012963
• Aliases: None
• Description: betaine--homocysteine S-methyltransferase 2 [Source:HGNC Symbol;Acc:1048]

Sequence

>retro_ttru_489
CTGCGCGATGGCCCTGGAGCCAAGAAGGGCATTTTAGAGTCTCTGGATAGCGGGGAGGGTGTGCTTGGAGACGGCAGCTT
TCGCATAACTCTGGAGAAGAGGGGCTACGTGAAGGCCGGGCTCTGGACTCCAGAAGCCATAGTAGGACATCCAAATGCAG
TTCGTCATCTTCACGTGGAGTTCTTGAGAGCGGGATAGAATGTCACGCGGACCTTCACCTTTTCTGCCAGTGAGGACAAT
ATGGAAAGCCAGTGGGAAGCTGTAAACGCCGCTGCCTGTGACCTTACCAGAGAAGCAGCCGACAGAGCTGACGCTTCAGT
CGCAGGGGGGATCTGCCAGACGTCGTTGTACAAACACCACAAGGATGAGGCTAGAATTTTAAAACTTTTTCGACTACAGC
TAGAGGTTTTTGCCAGGAAAAATGTGGACTTCTGGATTGCAGACTACTTTGAACACGTTGAAGAAGCTGCGTGGGCCGTG
GAAGTCTTAAAAGAATCCGGAAAACCCGTGGCAGCCACCGTGTGCATAGGCCCAGAGAGAGACATGCATGGTGTAACACC
TGGAGAATGTGGTGGAAGCTGGTGAAGGCGGGGGCTTCAGTCGTTGGCGTGAACTGCCGATGTGGGCCCTGGACCAGCCT
GAAGACAATGAGACTCATGAAGGAAGACCTGCGGGCTACAGGGCTGAAAGCACACTTGATGGTGCAGTCCCTGGGGTTCC
ACCTGCCCGACTGAGGCAAAAGAGGGTTTGTGGATCTCCTCGAATATCCCTTCGCACTGGAGCCCAGAGTTGCAACCAGA
TGGGATATTCAAAAATACGCCAGAGAGGCTTACAACCTGGGGGTCAGGTACATAAGGCGGGTGCTGTGGATTTGAGCCCT
CCCACATCAGGGCGATAGCAGAGGAGCTGGCCCTGGAAGGGGGATTTTTGCCTCTGTCTTCTGACAAACGTGGCAGCTGG
GGAAGTGGTCTCAGCACACACACCAAACCCTGGGTTAGAGCCAGGGCCAGATGAGAGTGTTGGGAGAATCTGCTGCCGAC
TTCGGGCAGACCTTTCTGCCCTTCAGTGTTAAAGCCAGATGCC

Alignment

ORF - retro_ttru_489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.54 %
• Parental protein coverage: 99.45 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LAGSSGVKKGILERLDSGEVVVGDGSFLITLEKRGYVKAGLWTSEAVVHAP--FRQLHMEFLRAGSNVMQ
          L....G.KKGILE.LDSGE.V.GDGSF.ITLEKRGYVKAGLWT.EA.V..P...R.LH.EFLRAG.NV..
Retrocopy LRDGPGAKKGILESLDSGEGVLGDGSFRITLEKRGYVKAGLWTPEAIVGHPNAVRHLHVEFLRAG*NVTR

Parental  TFTFSASEDKMESQWEAVNTAACDLAREVANKGDALVAGGICQTSLYKHHKDEARIKKLFRQQLEVFTRK
          TFTFSASED.MESQWEAVN.AACDL.RE.A...DA.VAGGICQTSLYKHHKDEARI.KLFR.QLEVF.RK
Retrocopy TFTFSASEDNMESQWEAVNAAACDLTREAADRADASVAGGICQTSLYKHHKDEARILKLFRLQLEVFARK

Parental  NVDFLIAEYFEHAEEAVWAVEVLKEARKPVAATMCIGPEGDMHGVTPGECA-VKLVKAGASIVGVNCRFG
          NVDF.IA.YFEH.EEA.WAVEVLKE..KPVAAT.CIGPE.DMHGVTPGEC...KLVKAGAS.VGVNCR.G
Retrocopy NVDFWIADYFEHVEEAAWAVEVLKESGKPVAATVCIGPERDMHGVTPGECG<WKLVKAGASVVGVNCRCG

Parental  PCTSLKTMRLMKEGLWASGLKAHLMVQPLGFHMPDCGKGGFVDLPEYPFALEPRVATRWDIQKYAREAYN
          P.TSLKTMRLMKE.L.A.GLKAHLMVQ.LGFH.PD.GK.GFVDL.EYPFALEPRVATRWDIQKYAREAYN
Retrocopy PWTSLKTMRLMKEDLRATGLKAHLMVQSLGFHLPD*GKRGFVDLLEYPFALEPRVATRWDIQKYAREAYN

Parental  LGVRYI-GGCCGFEPYHIRAIAEELAPERGFLPPSSDKHGSWGSGLNTHTKPWIRARARREYWENLLPAS
          LGVRYI.GGCCGFEP.HIRAIAEELA.E.GFLP.SSDK.GSWGSGL.THTKPW.RARAR.E.WENLLP.S
Retrocopy LGVRYI>GGCCGFEPSHIRAIAEELALEGGFLPLSSDKRGSWGSGLSTHTKPWVRARAR*ECWENLLPTS

Parental  GRPFCPSLSKPDA
          GRPFCPS..KPDA
Retrocopy GRPFCPSVLKPDA

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_489 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_489 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000007560	1 retrocopy	retro_cint_30,
Tursiops truncatus	ENSTTRG00000012963	1 retrocopy	retro_ttru_489 ,