Sequence
atgc intronic sequence ATGC exonic sequence...ctttatcatactttttttctaatgtgaagtatgagatgttatcttatcctcactatccaaaatttctgtttacgtcactttgtggtttttgaatgtgcagTTATATCATGGGTATTGGTGAAGCCGAGGCATTTTCTGAAAGGTTAAAAAGAGAGCTCCAGGCTCTGGAAGCAGCAAATGTGCATGCCATTTTAGAAAGT
Basic information
species | Glycine max |
transcript | GLYMA04G03710.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 6
ctttatca-tactttttttctaatgtgaa--gtatgagatgttatcttatcctcactatccaaaatttctgtttacgtcactttgtggtttttgaatgtgcagTTATATCATGGGTATTGGTGAAGCCGAGGCATTTTCTGAAAGGTTAAAAAGAGAGCTCCAGGCTCTGGAAGCAGCAAATGTGCATGCCATTTTAGAAAGT
|| | | || || | || | | || ||| | |||||| ||| | ||| | | || | |||| | | | || | ||||||| | ||||| ||||||||||| |||||||||||||||||| | || |||||||||| || || ||||| |||||||| ||||| ||| | |||||
-ttgagaactagcttgctggggatatcgatagtgggagcagatatcttttccac-ttattttaccagaatattca-gtcaactaatataaatgtcatatacagTTATGTAATGGGCATTGGTGAAGCTGAGGCATTTTCTGAAAGGCTGAAGCGAGAGCTCCAAGCGCTTGAAGCGGCAAATGTACATGCAATTCTTGAAAGC
upper sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 6
---ctttatcatactttttttctaatgtgaagtatgagatgttatcttatcctcactatccaaaatttctgtttacgtcactttgtggtttttgaatgtgcagTTATATCATGGGTATTGGTGAAGCCGAGGCATTTTCTGAAAGGTTAAAAAGAGAGCTCCAGGCTCTGGAAGCAGCAAATGTGCATGCCATTTTAGAAAGT
|| | | || | || | | | || | ||||| || | ||| | || || ||| | | || || | ||||||| | || || ||||||||||| |||||||||||||||||| | ||| ||||||| ||||| || ||||| |||||||| ||||| ||| | |||||
gagaactagcttgctggggataaaaag-ataatggaagcagatatct-attccacttattttgtcagattattcac-tcaactaatataattgtcatatacagTTATGTGATTGGCATTGGTGAAGCTGAGGCATTTTCTGAAAGGCTGAAACGAGAGCTTCAGGCGCTTGAAGCGGCAAATGTACATGCAATTCTGGAAAGC
upper sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 6
-ctttatcatactttttttctaatgtgaagtatgagatgttatcttatcctcacta-tccaa--aatttctgtttacgtcactttgtggtttttgaatgtgcagTTATATCATGGGTATTGGTGAAGCCGAGGCATTTTCTGAAAGGTTAAAAAGAGAGCTCCAGGCTCTGGAAGCAGCAAATGTGCATGCCATTTTAGAAAGT
| | || | ||| | | | | | | ||| | |||| | ||| || ||||| | ||| | ||| | || ||||||||| ||||||||||||||||||| ||||| |||||||||||||| || ||||| || | || |||||||||||||||||||||||||||| ||| |
aagccaacttagcatccttcccacattagtttctctgtcattacttgttgaaactacttcaatcaagttctgacaatttcagtc-atggcat---gatatgcagTTATGTCATGGGTATTGGTGAAGCTGAGGCCTTTTCTGAAAGGTTGAAGAGAGAACTTCTTGCCTTGGAAGCAGCAAATGTGCATGCCATTTTGGAATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcctcactatccaaaatttctgtttacgtcactttgtggtttttgaatgtgcagTTATATCATGGGTATTGGTGAAGCCGAGGCATTTTCTGAAAGGTTAAAAAGAGAGCTCCAGGCTCTGGAAGCAGCAAATGTGCATGCCATTTTAGAAAGT
tcctcac putative branch site (score: 2)
aaaatttctgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttatcatactttttttctaatgtgaagtatgagatgttatcttatcctcactatccaaaatttctgtttacgtcactttgtggtttttgaatgtgcagTTATATCATGGGTATTGGTGAAGCCGAGGCATTTTCTGAAAGGTTAAAAAGAGAGCTCCAGGCTCTGGAAGCAGCAAATGTGCATGCCATTTTAGAAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - atccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttgtg