RetrogeneDB ID: retro_ttru_1353

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_111264:266282..266742(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFT2D1
• Ensembl ID: ENSTTRG00000004447
• Aliases: None
• Description: SFT2 domain containing 1 [Source:HGNC Symbol;Acc:21102]

Sequence

>retro_ttru_1353
AAGCTGCAGAGGTTCCTGAGTGACCAGGGTGACAAAGAGCGTAGCCTGACCACAGAGATCCTGGATGTTTGGTCCCTTAG
CTTTAATACCAGATTGAGGTGGTCTGGTATATGCTTTGTATGCAGCATTTTCTATTCTATCCTTGGAACTGGATTGCTAT
GGCTTCCTGGTGGCATAAAAGTTTTGGCAGTGTTTTAGAGCCTGGGAAATAATCCTGCATGAGTCAGTATGAGTTTTTTA
ATGGGCTCTGTGAAGCAACTGACGAAAATATTTGAAACAAGATTGCCTGCAACAATTATTATTCTTTTTTGTTTGTTTCA
TATTTACACTGTGTGCTTATTTTTGGTCACATAAGAAGGGAATGAATATGTTGCAGTTCTTGTGAAGAGCCTAATATAGT
CTATCATGCATCTTATATGCAAAAGATGCAGTCATGAAAGGCTATTTTTCTCTCCTAAGT

Alignment

ORF - retro_ttru_1353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.86 %
• Parental protein coverage: 98.74 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLRRVLSGQDDEEQGLTAQVLDASSLSFNTRLKWFAICFASGIVFSILGTGLLWLPGGIKLFAVFYTLGN
          KL.R.LS.Q.D.E..LT...LD..SLSFNTRL.W..ICF...I..SILGTGLLWLPGGIK..AVF..LGN
Retrocopy KLQRFLSDQGDKERSLTTEILDVWSLSFNTRLRWSGICFVCSIFYSILGTGLLWLPGGIKVLAVF*SLGN

Parental  IAALASTCFLMGPVKQLKKMFETTRLLATIVMLLCF-ILTLCAALWW-HKKGLALLFCILQFLSMTWYSL
          ..A..S..FLMG.VKQL.K.FE.TRL.ATI..L.C........A..W.HKKG...L....QFL....YSL
Retrocopy NPA*VSMSFLMGSVKQLTKIFE-TRLPATIIILFCL>FIFTLCAYFWSHKKGMNML----QFL*RA*YSL

Parental  SYIPYARDAVIKCCSSLLS
          S.I.YA.DAV.K...SLLS
Retrocopy SCILYAKDAVMKGYFSLLS

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_1353 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1353 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 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009311	3 retrocopies	retro_amel_1244, retro_amel_1452, retro_amel_374,
Bos taurus	ENSBTAG00000002993	5 retrocopies	retro_btau_1458, retro_btau_1460, retro_btau_31, retro_btau_546, retro_btau_900,
Canis familiaris	ENSCAFG00000000811	2 retrocopies	retro_cfam_283, retro_cfam_551,
Equus caballus	ENSECAG00000019479	1 retrocopy	retro_ecab_1029,
Mus musculus	ENSMUSG00000073468	1 retrocopy	retro_mmus_164,
Oryctolagus cuniculus	ENSOCUG00000001200	1 retrocopy	retro_ocun_1492,
Otolemur garnettii	ENSOGAG00000006302	1 retrocopy	retro_ogar_1601,
Ochotona princeps	ENSOPRG00000003408	2 retrocopies	retro_opri_37, retro_opri_809,
Pongo abelii	ENSPPYG00000017165	1 retrocopy	retro_pabe_181,
Sus scrofa	ENSSSCG00000004020	1 retrocopy	retro_sscr_751,
Tupaia belangeri	ENSTBEG00000000045	2 retrocopies	retro_tbel_3277, retro_tbel_747,
Tursiops truncatus	ENSTTRG00000004447	2 retrocopies	retro_ttru_1353 , retro_ttru_624,