Sequence
atgc intronic sequence ATGC exonic sequence...ttggcactcaaatcacctgtctagtttccaattatgttttctttaataaaaaatattatgaacataaaggtgtatgattttttaattcttgggtgtccagGTTCCATTTTTCGGCCAAATGGATGACCAGCTTCTAGATGCAATATGCGAACGTCTTGTGTCATCGTTAAACACAAAAGACACATACATCGTTCGCGAAG
Basic information
species | Glycine max |
transcript | GLYMA06G19570.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G19570.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g08060.t01 (Vitis vinifera), 3'ss of exon 5
ttggcactcaaatcacctgtctagtttccaattatgttttctttaataaaaaatattatg-aacataaaggtgtatgattttttaattcttgggtgt-ccagGTTCCATTTTTCGGCCAAATGGATGACCAGCTTCTAGATGCAATATGCGAACGTCTTGTGTCATCGTTAAACACAAAAGACACATACATCGTTCGCGAAG
| | | || | | | | || ||| | || |||||| || |||| | ||||| |||| || | | ||||||||| || ||| ||||||||||| ||||| ||||||| ||||| ||||||||||||||||| |||| ||| |||| |||| || ||||| ||||
-tctatcataggccag-tacttgatatataaaacagttgaaatggtctaagaatattgcctaatctaaatccgcttgattgacaaattgttacattttccagGTTCCTTTCTTCTCACAAATGGATGATCAGCTCTTAGATGCCATATGTGAACGTCTTGTGTCATCCTTAAGCACTCAAGATGCATATATTGTTCGGGAAG
upper sequence: GLYMA06G19570.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g08050.t01 (Vitis vinifera), 3'ss of exon 2
ttggcactcaaatcacctgtctagtttccaattatgttttctttaataaaaaatattatg-aacataaaggtgtatgattttttaattcttgggtgt-ccagGTTCCATTTTTCGGCCAAATGGATGACCAGCTTCTAGATGCAATATGCGAACGTCTTGTGTCATCGTTAAACACAAAAGACACATACATCGTTCGCGAAG
| | | || | | | | || || ||| || |||||| || |||| ||||| |||| || | | ||||||||| || ||| ||||||||||| ||||| ||||||| |||||||||||||| |||||||| |||| ||| |||| |||| || ||||| || |
-tctatcataggccaa-tacttgttgtgtaagacacttgaatttgtctaagaatattgcccaatctaaatccacttgattgacaaattgttacattttccagGTTCCTTTCTTCTCACAAATGGATGATCAGCTCTTAGATGCCATATGCGAACGTCTCGTGTCATCCTTAAGCACTCAAGATGCATATATTGTTCGGGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaaaaatattatgaacataaaggtgtatgattttttaattcttgggtgtccagGTTCCATTTTTCGGCCAAATGGATGACCAGCTTCTAGATGCAATATGCGAACGTCTTGTGTCATCGTTAAACACAAAAGACACATACATCGTTCGCGAAG
ttttaat putative branch site (score: 3)
aaatattatgaacata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttggcactcaaatcacctgtctagtttccaattatgttttctttaataaaaaatattatgaacataaaggtgtatgattttttaattcttgggtgtccagGTTCCATTTTTCGGCCAAATGGATGACCAGCTTCTAGATGCAATATGCGAACGTCTTGTGTCATCGTTAAACACAAAAGACACATACATCGTTCGCGAAG
- - cactcaa
- - - - - - -cacctgt
- - - - - - - - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatga