RetrogeneDB ID: retro_ttru_1119

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_104090:171008..172011(+)
• 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_1119
AGGGCGCCGCTGCCTGGCGGCGCCAACGAGGCCCGGCAGAGGCGCCCCCGTTACACCCCCTGCCCCCGGGGCGCTGCCGG
CCCTCTGCGACACCAGTCGCCTGGCGCACCGGCTTTTGGCACAGTTGCTGATATGCTTCCTTGGTTTCGGTGGCTATTTT
TGCTATGATAATCCTGCTGCCCTTCAGACTCAGGTTAAACGGGATATGCAGGTGAATACCACGAAATTCATGCTGCTGTA
TGCCTGGTATTCTTGGCCCAATGTAGCTTTGTGTTTCTTTGGTGGCTTTTTGGTAGACCGCGTATTTGGAATACGATGGG
GCACCATTATTTTTAGTTGCTTTGTTTGCGTTGGACAGGTTGTTTTTGCTCTGGGTGGAATATTTCGTGCTTTTTGGCTG
ATGGAATTTGGAAGGTTTGTGTTTGGGATTGGTGGGGAGTCCTTAGCAGTTGCCCAGAATACATATGCTGTGAGTTGGTT
TAAAGGCAAAGAATTAAACTTGGTGTTTGGACTCCAGCTAAGCATGGCTAGAACTGGAAGTACAGTAAACATGAACCTCA
TGGGGTGGCTGTATTATAAGGTTGAAGCTTAGTTGGGTTCTGCTGGTCACACAACCCTTGGGGTCACACTTACGATCGGG
GGTATAACATGTCTTCTTTCACTAGTCTGTGCCTTGGCCCTTGCTTACTTGGATCAGAGAGCAGAACGAATCCTTCGTAA
AGAGCAAGGAAAAACGGGTGAAGTTATCAAGTTAACTGATGTGAAGGACCTCTCCTTCCCCCTGTGGCTCATATTCATCA
TCTGTGTCGGCTATTATGTTGCTGTGTTCCCGTTCACTGGACTTGGGAAAGTTTTCTTTACAGAGAAATTTGGCTTTTCC
TCCCAGGCAGCGAGTGCTGTTAACAGTATTGTATATGTAATATCAGCTCCCATGTCCCCCATATTTGGGCTTCTGGTGGA
TAAAACAGGAAGGAACATCATCTGGGTTCTGTGTGCAGTGGTG

Alignment

ORF - retro_ttru_1119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.43 %
• Parental protein coverage: 71.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RALLPGG-PDKAGRGAPVTPPAPGALPALCDPSRLAHRLLVLLLMCFLGFGSYFCYDNPAALQTQVKRDM
          RA.LPGG.P...GRGAPVTPPAPGALPALCD.SRLAHRLL..LL.CFLGFG.YFCYDNPAALQTQVKRDM
Retrocopy RAPLPGG>PTRPGRGAPVTPPAPGALPALCDTSRLAHRLLAQLLICFLGFGGYFCYDNPAALQTQVKRDM

Parental  QVNTTKFMLLYAWYSWPNVVLCFFGGFLVDRVFGIRWGTIIFSCFVCVGQVVFALGGIFNAFWLMEFGRF
          QVNTTKFMLLYAWYSWPNV.LCFFGGFLVDRVFGIRWGTIIFSCFVCVGQVVFALGGIF.AFWLMEFGRF
Retrocopy QVNTTKFMLLYAWYSWPNVALCFFGGFLVDRVFGIRWGTIIFSCFVCVGQVVFALGGIFRAFWLMEFGRF

Parental  VFGIGGESLAVAQNTYAVSWFKGKELNLVFGLQLSMARIGSTVNMNLMGWLYSKVEASLGSAGHTTLGVT
          VFGIGGESLAVAQNTYAVSWFKGKELNLVFGLQLSMAR.GSTVNMNLMGWLY.KVEA.LGSAGHTTLGVT
Retrocopy VFGIGGESLAVAQNTYAVSWFKGKELNLVFGLQLSMARTGSTVNMNLMGWLYYKVEA*LGSAGHTTLGVT

Parental  LIIGGITCILSLVCALALAYLDQRAERILHKEQGKTGEVIKLTDVKDFSFPLWLIFIICVGYYVAVFPFI
          L.IGGITC.LSLVCALALAYLDQRAERIL.KEQGKTGEVIKLTDVKD.SFPLWLIFIICVGYYVAVFPF.
Retrocopy LTIGGITCLLSLVCALALAYLDQRAERILRKEQGKTGEVIKLTDVKDLSFPLWLIFIICVGYYVAVFPFT

Parental  GLGKVFFTEKFGFSSQAASAINSIVYVISAPMSPIFGLLVDKTGKNIIWVLCAVV
          GLGKVFFTEKFGFSSQAASA.NSIVYVISAPMSPIFGLLVDKTG.NIIWVLCAVV
Retrocopy GLGKVFFTEKFGFSSQAASAVNSIVYVISAPMSPIFGLLVDKTGRNIIWVLCAVV

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_1119 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1119 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,