Sequence
atgc intronic sequence ATGC exonic sequence...agacactgtcagagccatagatcccaataagtgttgttaatgtcattgataaattattatttttttgttgattatgggactcatttttttaaaacattagGTCTGGGCGCAGCATGGAATGTTGCTGACGTGTCAAAAGGATCAACTGTGGTGATTTTTGGTCTTGGAACTGTTGGCCTATCT
Basic information
species | Glycine max |
transcript | GLYMA16G23820.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G23820.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G24760.1 (Arabidopsis thaliana), 3'ss of exon 4
agacactgtcagagccatagatcccaataagtgttgttaatgtcattga---taaattattatttttttgttgattatgggactcatttttttaaaacattagGTCTGGGCGCAGCATGGAATGTTGCTGACGTGTCAAAAGGATCAACTGTGGTGATTTTTGGTCTTGGAACTGTTGGCCTATCT
||| | || | |||| |||| || || | || ||||| | | || | || || || | | |||| |||||||| || |||||||||||||||||||| || |||||| |||| ||| ||||| ||||||||||||||||| || || |||
----------------gtagttaaaaaataatgtttttaaagtgatgaaatgccaacaattatctata-gtcagtactgagaatcttgggtgtaaat--ttagGTCTTGGTGCAGCATGGAATGTTGCTGATGTACAAAAAGGTTCAAGTGTTGTGATATTTGGTCTTGGAACTGTCGGTCTTTCT
upper sequence: GLYMA16G23820.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0039g00320.t01 (Vitis vinifera), 3'ss of exon 4
agacactgtcagagccatagatcccaataagtgttgttaatg--tcattgataaattattatttttttgttgattatgggactcatttttttaaaacattagGTCTGGGCGCAGCATGGAATGTTGCTGACGTGTCAAAAGGATCAACTGTGGTGATTTTTGGTCTTGGAACTGTTGGCCTATCT
|| | | | | | | ||| || | || | | || | || || ||| || ||| || | ||| | |||||||| || ||||| ||||| ||||| | | | ||||||||||||| || |||||||| ||||||||||||||||| |||
--gcatattaacttgaacaacgtttattcagttttatgtctggttagatcatgagtttttggtttgggtaagaatatttaacaagtggaattatattgttagGTCTAGGAGCAGCTTGGAAGGTTGCCAATATAACCGAAGGATCAACTGTAGTCATTTTTGGACTTGGAACTGTTGGCCTTTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgataaattattatttttttgttgattatgggactcatttttttaaaacattagGTCTGGGCGCAGCATGGAATGTTGCTGACGTGTCAAAAGGATCAACTGTGGTGATTTTTGGTCTTGGAACTGTTGGCCTATCT
tgttgat putative branch site (score: 4)
ttttttta putative PPT
aaattattattttttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agacactgtcagagccatagatcccaataagtgttgttaatgtcattgataaattattatttttttgttgattatgggactcatttttttaaaacattagGTCTGGGCGCAGCATGGAATGTTGCTGACGTGTCAAAAGGATCAACTGTGGTGATTTTTGGTCTTGGAACTGTTGGCCTATCT
- - actgtca
- - - - - - - - - - atcccaa
- - - - - - - - - - - - - - - -tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat