RetrogeneDB ID: retro_ttru_624

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2930:208509..208961(+)
• Located in intron of: ENSTTRG00000016202

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_624
TCTGGGTTTCTTGATGGACATGAGGGGCTGGTGGACAGGTCCTGGATGCCTCTTCCCTCCATTTCAACACCAGCATGAAG
TGGTGTGTCATATGCTTTCTATGGGCATTTTCTGTTGTCTCATTGGAACTGGATTACTGTGGCTTCCTGGTGGCATAAAA
CTTTTTGCAGTGTTTTATACCTTTGCCAATATTGCTGTACTCTCCAGTATATGCTTTTTAATGGCATTCATGAAGCAAAT
GAAGAAAATGTTTGAAACAAAAAGATGGCTTGTACAATTGTTATGTGTTTGTGATTGTTATTTAGGTCCTGTATACTGCT
CTTTGGTGGCATAGGAGGAGACTGGCCTTATGATTCTGCATTTTGAAGCTCTTGTCAAAGATCTGGCATAGTCTATTATA
CATCCCATATGCAAGTGTTGCAGTAATTAAATGCTGTTCTTTTCTCCTTAGT

Alignment

ORF - retro_ttru_624 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.18 %
• Parental protein coverage: 94.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SGQDDEEQGLT-AQVLDASSLSFNTRLKWFAICF-ASGIVFSILGTGLLWLPGGIKLFAVFYTLGNIAAL
          SG..D...GL...QVLDASSL.FNT..KW..ICF...GI.....GTGLLWLPGGIKLFAVFYT..NIA.L
Retrocopy SGFLDGHEGLV<GQVLDASSLHFNTSMKWCVICF<SMGIFCCLIGTGLLWLPGGIKLFAVFYTFANIAVL

Parental  ASTCFLMGPVKQLKKMFETTRLL-ATIVMLLCFILTLCAALW-W-HKKGLALLFCILQFLSMTWYSLSYI
          .S.CFLM...KQ.KKMFET.R.L..TIVM.L......C..L..W.H...LAL.FCIL..LS..W.SL.YI
Retrocopy SSICFLMAFMKQMKKMFETKRWL<CTIVMCL*LLFRSCILLF<WWHRRRLAL*FCILKLLSKIWHSLLYI

Parental  PYARDAVIKCCSSLLS
          PYA..AVIKCCS.LLS
Retrocopy PYASVAVIKCCSFLLS

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_624 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_624 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 ,