Sequence
atgc intronic sequence ATGC exonic sequence...atttccttatgttctttgttcaatattaggaacaaaagttctcagtaagccaataattctgacttcctttgttggcgtgcttaaaatattcgaatgtcagGTTTGGAGACTCCAGGCAGCTCTTGGTGAACAAACAGAAATTACAAAATTCAGCCAACAGGAGTATGAAAGACTTCAAAAT
Basic information
species | Glycine max |
transcript | GLYMA05G07960.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G07960.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G18470.1 (Arabidopsis thaliana), 3'ss of exon 11
-------------------atttccttatgttctttgttcaatattaggaacaa----aagttctcagtaagccaataattctgacttcctttg---ttggcgt-gcttaaa--------atattcga---------atgtc---agGTTTGGAGACTCCAGGCAGCTCTTGGTGAACAAACAGAAATTACAAAATTCAGCCAACAGGAGTATGAAAGACTTCAAAAT
|||| || | ||| |||| | | | || | |||||| | | | | ||| ||| | | | || | |||||| |||| | || || |||| |||||||| || ||||| |||||||||||||||||||| |||||||||||||| ||||| ||||||||||| ||||||
gtaactttacctctctggcatttttttgt-ttcccaattcagtgctgatattaactttaggttctc--tttgttgttgaatcttgtttcttctagtttcagcattgcttaagtgttgtttgcattcaatctaatttgatatctctagGTGTGGAGACTTCAAGCAGCACTTGGTGAACAAACAGAAATCACAAAATTCAGCCAGCAGGAATATGAAAGACTGCAAAAT
upper sequence: GLYMA05G07960.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G73950.1 (Arabidopsis thaliana), 3'ss of exon 11
----------------------------------atttccttatgttctttgttcaatattaggaacaaaagttctcagtaagccaataattctgacttcctttgttggcgtgcttaaaatattcgaatgtcagGTTTGGAGACTCCAGGCAGCTCTTGGTGAACAAACAGAAATTACAAAATTCAGCCAACAGGAGTATGAAAGACTTCAAAAT
|| || | || |||||| | | |||| || | | || | | | | || ||| | || ||| | |||||||| |||||||| || ||||| |||||||||||||||||||| || |||||||| || ||||| ||||| ||||| ||||||
gtattttgccttttttctcttacatgcaaatatgtcgtcgtttttttgtttgttaagtcttagatctctggtatcattattactcagtgctgttcatgtctttttgtatttgatctataattt---ggtgtcagGTGTGGAGACTTCAAGCAGCACTTGGTGAACAAACAGAAATCACGAAATTCAGTCAGCAGGAATATGAGAGACTGCAAAAT
upper sequence: GLYMA05G07960.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv17s0000g04160.t01 (Vitis vinifera), 3'ss of exon 11
--------------------atttccttatgttctttgttcaatattaggaacaaaagttctcagtaagccaataattctgacttcctttgttggcgtgcttaaaat---attcgaatg---------------tcagGTTTGGAGACTCCAGGCAGCTCTTGGTGAACAAACAGAAATTACAAAATTCAGCCAACAGGAGTATGAAAGACTTCAAAAT
||| | || | || | || || | | |||||| ||| | | | || |||| | || |||| | | | || || ||| | || ||||| |||||||| || || || |||||||| ||| ||||||| ||||| | ||| | ||||||||||||||||||||||||
gtgatcatagttctcatagcattcctttgtaca-ttaccttaaaatctgaagttaaagttttcaatttac-attatttctaaatttttttgctatcatagttctgatttcatttgtattattggtttttttctcccagGTGTGGAGACTTCAAGCTGCACTTGGTGAGCAATCAGAAATCACAAAGTACAGTAAGCAGGAGTATGAAAGACTTCAAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagccaataattctgacttcctttgttggcgtgcttaaaatattcgaatgtcagGTTTGGAGACTCCAGGCAGCTCTTGGTGAACAAACAGAAATTACAAAATTCAGCCAACAGGAGTATGAAAGACTTCAAAAT
ttctgac putative branch site (score: 2)
ttaaaatattcgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttccttatgttctttgttcaatattaggaacaaaagttctcagtaagccaataattctgacttcctttgttggcgtgcttaaaatattcgaatgtcagGTTTGGAGACTCCAGGCAGCTCTTGGTGAACAAACAGAAATTACAAAATTCAGCCAACAGGAGTATGAAAGACTTCAAAAT
- - ccttatg
- - - - - - - - - - - - - - - aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcgtgc