RetrogeneDB ID: retro_ttru_397

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2135:194232..195085(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTHFD2L
• Ensembl ID: ENSTTRG00000002366
• Aliases: None
• Description: methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like [Source:HGNC Symbol;Acc:31865]

Sequence

>retro_ttru_397
ATCAAGCAGGAAGTGCAGCAGGAGCTGGAAGCGTGGGTGGTGTCAGGCAACAAAGGACCACACCTGAGCGCGGTTTTGGT
TGGCGAGAATCCCGCAAGTCACTCCTCTGTCCTCCACAAAACCAGAGTAGCTGCCGATGTGGGAATCAACCGTGAGACAA
TTGTGAAACCAGCTTCAATTTCAGAGGAAGAACTGTTGAATTTAATCAATAAACTAAATAATGATGATAATGTAGATGGC
CTCCTCGTTCAGCTGCCTCTTCCAGAGCACATTGATGAGAGAAAGATCTGCAATGCTGTTTCTCCAGACAAAGATGGTGA
TGGCTTTCATGTAATTAACATAGGGCGAATGTGTTTGGACCAGAATTCCATGTTACCAGCTACTCCATGGGGTATGTAGG
AAATAATTAAGCAAACTGGCATTCCAACCCTAGGGAAGAATGTGGGTGTGGATGGAAGGTTAAAAAATGTTGGAGTGCCC
ATTGCAGTGTTACTACACACCGGAGGGGCACACAAACATCCTGGAGGTGATGCCGCTGTCATAATTTCTCATCCATACAC
TCCCAAGGAGCAGCTGAAGAAACATACAGCTCTTGCAGATATTGTCGTCTCCGCTGCAGGCATTCCAAATCTGATCACAG
CCAATATGATTAAGGAAGGAGCAGCTGTCATTGATGTGGGAATAAATAGAATTCAAGATCCCATAACTGCTAAACCCAAG
TTGGTTGGAGATGTGGATTTTGACGGAGTCAGGAAGAAAGCCGGTTACATCACTCCAGTCCCTGGGGGGTGTTTGTCCCA
TGACAGTGGCAATGCTAATGAGGAATACCATTACTTCTGCGAAAAAAGTGCTG

Alignment

ORF - retro_ttru_397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.75 %
• Parental protein coverage: 98.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IQKEIQRGV-SWISLGNGRPHLSIILVGDNPASHTYVRKKIKAAAAVGICSEIILKPKDVSQEELLDITN
          I..E.Q.....W...GN..PHLS..LVG.NPASH..V..K...AA.VGI..E.I.KP...S.EELL...N
Retrocopy IKQEVQQELEAWVVSGNKGPHLSAVLVGENPASHSSVLHKTRVAADVGINRETIVKPASISEEELLNLIN

Parental  QLNMDPRVSGILVQLPLPDHVDERTVCNGIAPEKDVDGFHIINIGRLCLDQHSLIPATASAVWEIIKRTG
          .LN.D..V.G.LVQLPLP.H.DER..CN...P.KD.DGFH.INIGR.CLDQ.S..PAT.....EIIK.TG
Retrocopy KLNNDDNVDGLLVQLPLPEHIDERKICNAVSPDKDGDGFHVINIGRMCLDQNSMLPATPWGM*EIIKQTG

Parental  IETLENIVVVAGR-SNAGMPIAMLLHTDGEHR-PGGDATVTIAHRYTPKEQLKIHTLLADVIVVAAGIPK
          I.TL...V.V.GR..N.G.PIA.LLHT.G.H..PGGDA.V.I.H.YTPKEQLK.HT.LAD..V.AAGIP.
Retrocopy IPTLGKNVGVDGRLKNVGVPIAVLLHTGGAHKHPGGDAAVIISHPYTPKEQLKKHTALADIVVSAAGIPN

Parental  LITSDMVKEGAAVIDVGINYVHDPMTGKTKLVGDVDFEAVKKKASFITPVP-GGVGPMTVAMLLKNTLLA
          LIT..M.KEGAAVIDVGIN...DP.T.K.KLVGDVDF..V.KKA..ITPVP.GGV.PMTVAML..NT...
Retrocopy LITANMIKEGAAVIDVGINRIQDPITAKPKLVGDVDFDGVRKKAGYITPVP>GGVCPMTVAMLMRNTITS

Parental  AKKII
          AKK..
Retrocopy AKKVL

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_397 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_397 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006627	1 retrocopy	retro_chof_2362,
Callithrix jacchus	ENSCJAG00000013883	1 retrocopy	retro_cjac_1764,
Tupaia belangeri	ENSTBEG00000009980	4 retrocopies	retro_tbel_2436, retro_tbel_2590, retro_tbel_3051, retro_tbel_850,
Tursiops truncatus	ENSTTRG00000002366	1 retrocopy	retro_ttru_397 ,