RetrogeneDB ID: retro_ttru_1271

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_109249:137356..138681(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFSD1
• Ensembl ID: ENSTTRG00000002207
• Aliases: None
• Description: major facilitator superfamily domain containing 1 [Source:HGNC Symbol;Acc:25874]

Sequence

>retro_ttru_1271
GAGGATGAGGAAGCAGGGGCACCGCTTCCTGGCGGCCCCAACGAGGCCAGCAGAGGCGCCCCCGTTACCTCCCCCTGTCC
CCGGGGCGCTGCCGGCCCTCTGCAACCCCAGTCACCTGGCGCACCAGCTTTTGGTGCTGTTGCTTCCTTGGTTTCTGCAG
CTGGTTTTGCTATGATAATCCTGCTGCCCTTCAGACGCAGGTTAAACGGGATATTCAGGTGAATACCACGAAATTCATGA
CGCTGTATGCCTGGTATTCTTGGCCCAATGTAGTTTTGTGTTTCTTTGGTGGCTTTTTGATAGACTGCGTATCTGGAATA
CAATGGGGCGCCGTTATGTTTAGTCGCTTTGTTTGCGTTGGACAGGTTGTTTTTTGCTCTGGGTGGAATATTTCACGCTT
TTTGGCTGATGGAATTTAGAAGGTTTGTTTGGGATTGGTGGGGAGTCCTTAGCAGTTGCCCAGAATACCTATGCTGTGAG
TTGGTTTAAAGGCAAAGAATTAAACTTGGTGTTTGGACTCCAACTGAGCATGGCTAGAACTGGAAGTACAGTAAACATGA
ACCCCATGGGATGGCTGTATTCTAAGGTTGAAGCTTCATTGGGTTCTGCTGGTCACACAACCCTTGGGGTCACACTTATG
ATCGGGGGTATAACATGTCTTCTTTCACTAGTCTGTGCCTTGGCCCTTGCTTACTCGGATCAGAGAGCAGAATGAATCCT
TCGTAAAGAGCAAGGAAAAACAGCTGAAGTTATCAAGTTCACTGATGTGAAGGACTTCTCCTTCCCCCTGTGGCTCATAT
TCATCATCTGTGTCTGCTATTATGTTGCTGTGTTCCCTTTCACTGGACTTGGGCAAGTTTTCTTACAGAGAAATCTGGCT
TTTCCTCCCAGGCAGCGAGTGCTATTAACAGTATTGTGTATGTAACATCAGCTCCCATGTCCCCAATATTTGGGCTTCTA
GTGGATAAAACAGGAAAGAACATCATCTGGGTTCTGTGTGCAGTGGTGACCACTCTTGCTTCCCATATGATGCTGGCCTT
CAGGTTGTGGAACCCTTGGATTGCTATGTGTCTCCTGGGACTCTCTACTCATTGCCTGCCTGTACATTGTGGCCAATGGT
GGCATTTGTAGTTCCCTAACATCAACTGGGAACTGCATACGGCTTCATGCAGTCCATTCAGAATCTTGGGTTGGCAGTCA
TTTCCATCATTGCTGGCATGATATTGAATATTTGGGGATATCTGTTTTTAGAAGTTTTCTTCATTGCCTGTGTTTCTTTC
TCGCTTTTATCTGTGGTCTTACTCTACTTGGTGAATCGTGCCCAA

Alignment

ORF - retro_ttru_1271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.4 %
• Parental protein coverage: 95.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  EEEEVRALLPGGPDKAGRGAPVT-PPAPGALPALCDPSRLAHRLLVLLLM-CFLGFGSYFCYDNPAALQT
          E.EE..A.LPGGP..A.RGAPVT.PP.PGALPALC.P....H....LL...CFLGF.S.FCYDNPAALQT
Retrocopy EDEEAGAPLPGGPNEASRGAPVT>PPVPGALPALCNP---SHLAHQLLVL>CFLGFCSWFCYDNPAALQT

Parental  QVKRDMQVNTTKFMLLYAWYSWPNVVLCFFGGFLVDRVFGIRWGTIIFSCFVCVGQVV-FALGGIFNAFW
          QVKRD.QVNTTKFM.LYAWYSWPNVVLCFFGGFL.D.V.GI.WG...FS.FVCVGQVV.FALGGIF.AFW
Retrocopy QVKRDIQVNTTKFMTLYAWYSWPNVVLCFFGGFLIDCVSGIQWGAVMFSRFVCVGQVV>FALGGIFHAFW

Parental  LMEFGRFVF-GIGG-ESLAVAQNTYAVSWFKGKELNLVFGLQLSMARIGSTVNMNLMGWLYSKVEASLGS
          LMEF.RFV..G..G.ESLAVAQNTYAVSWFKGKELNLVFGLQLSMAR.GSTVNMN.MGWLYSKVEASLGS
Retrocopy LMEFRRFVW<GLVG<ESLAVAQNTYAVSWFKGKELNLVFGLQLSMARTGSTVNMNPMGWLYSKVEASLGS

Parental  AGHTTLGVTLIIGGITCILSLVCALALAYLDQRAERILHKEQGKTGEVIKLTDVKDFSFPLWLIFIICVG
          AGHTTLGVTL.IGGITC.LSLVCALALAY.DQRAE.IL.KEQGKT.EVIK.TDVKDFSFPLWLIFIICV.
Retrocopy AGHTTLGVTLMIGGITCLLSLVCALALAYSDQRAE*ILRKEQGKTAEVIKFTDVKDFSFPLWLIFIICVC

Parental  YYVAVFPFIGLGKV-FFTEKFGFSSQAASAINSIVYVISAPMSPIFGLLVDKTGKNIIWVLCAVVTALAS
          YYVAVFPF.GLG.V.F.TEK.GFSSQAASAINSIVYV.SAPMSPIFGLLVDKTGKNIIWVLCAVVT.LAS
Retrocopy YYVAVFPFTGLGQV<FLTEKSGFSSQAASAINSIVYVTSAPMSPIFGLLVDKTGKNIIWVLCAVVTTLAS

Parental  HMMLAFTLWNPWIAMCLLGLS-YSLLACALWPMVAFVVPEHQLGTAYGFMQSIQNLGLAVISIIAGMILD
          HMMLAF.LWNPWIAMCLLGLS.YSL.AC.LWPMVAFVVP.HQLGTAYGFMQSIQNLGLAVISIIAGMIL.
Retrocopy HMMLAFRLWNPWIAMCLLGLS<YSLPACTLWPMVAFVVP*HQLGTAYGFMQSIQNLGLAVISIIAGMILN

Parental  TWGYLFLEVFFIACVSFSLLSVLLLYLVNRAQ
          .WGYLFLEVFFIACVSFSLLSV.LLYLVNRAQ
Retrocopy IWGYLFLEVFFIACVSFSLLSVVLLYLVNRAQ

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_1271 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1271 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009263	1 retrocopy	retro_btau_1323,
Dasypus novemcinctus	ENSDNOG00000005048	1 retrocopy	retro_dnov_1121,
Macaca mulatta	ENSMMUG00000023510	1 retrocopy	retro_mmul_1210,
Oryctolagus cuniculus	ENSOCUG00000001272	1 retrocopy	retro_ocun_1528,
Pongo abelii	ENSPPYG00000014247	1 retrocopy	retro_pabe_1427,
Tupaia belangeri	ENSTBEG00000013974	1 retrocopy	retro_tbel_1396,
Tursiops truncatus	ENSTTRG00000002207	2 retrocopies	retro_ttru_1119, retro_ttru_1271 ,
Drosophila melanogaster	FBgn0031636	1 retrocopy	retro_dmel_45,