Sequence
atgc intronic sequence ATGC exonic sequence...acacgcacacttttgttatctttatttgcctggaactttgtagttttccaacaataatttcagcattctgatatgagggttgttttattggatgttgcagAGGTATCATGTTGGATGATGACAGGAGAAAGACAAGCAGCAAGGATCCGTGGCTTGTACTTGAAAACTATATTGAAGCAGGACATTACCTTCTTTGACAC
Basic information
species | Glycine max |
transcript | GLYMA13G29380.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G086730_T01 (Zea mays), 3'ss of exon 2
acacgcacacttttgttatctttatttgcctggaactttgtagttttccaacaataatttcagcattctga-tatgagggttgttttattggatgtt---gcagAGGTATCATGTTGGATGATGACAGGAGAAAGACAAGCAGCAAGGATCCGTGGCTTGTACTTGAAAACTATATTGAAGCAGGACATTACCTTCTTTGACAC
| | || | | ||| | || |||| | | ||| | || | |||| || || | | || || |||||||||||||||||| || || |||||||||||||||||| | ||| | | |||||| | || | || | | ||||| ||| | ||||||||||
----gtaagattctaatttctcaaaatgaaaggaaacaaacgggacctaatggatattactagaaacaaacctatgtcaattaattaacttaatattttgctagAGGTATCATGTTGGATAATTACCGGAGAAAGACAAGCAGCACGAATCAGAGCCTTGTATCTCAAGGCAATTCTAAGACAGGATATTGCATTCTTTGACAT
upper sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G082385_T01 (Zea mays), 3'ss of exon 2
---acacgcacacttttgttatctttatttgcctggaactttgtagttttccaacaataatttcagcattctgatatgagggttgttttattggatgttgcagAGGTATCATGTTGGATGATGACAGGAGAAAGACAAGCAGCAAGGATCCGTGGCTTGTACTTGAAAACTATATTGAAGCAGGACATTACCTTCTTTGACAC
|| || | | | | | ||| | || | ||| ||| || |||| | | | | || ||| |||||||| | | |||||| ||||||||||||| || ||||||||||||||||| | || || || | || | ||| || |||||| || |||||| | || |||||||
ctgccagaggcatctaaggtgttactctttttcattgttttgaggcactgccagttatagatt-agcactaaggtgttagtgtt-ttttattgttt-taatagAGGTTGCATGTTGGATGATCACTGGAGAAAGACAAGCAGCTCGCATACGAGGTCTCTATCTTAAAGCTCTATTGAGACAAGACATTGCATTTTTTGACAA
upper sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 2
acacgcacacttttgttatctttattt---gcctggaactttgtagttttccaacaataatttcagcattctgatatgagggt------tgttttattggatgttg---cagAGGTATCATGTTGGATGATGACAGGAGAAAGACAAGCAGCAAGGATCCGTGGCTTGTACTTGAAAACTATATTGAAGCAGGACATTACCTTCTTTGACAC
|| || | || | || | ||| || | | | | | | |||| | || || | || | ||| | ||| ||||||| || | |||||| | ||||| |||||||| ||| | |||| || || |||||||||||||| ||||||| |||||||| | |||||||||||
-----------ttcgtggttttgaatttaagtctgaaattgtctgacccaacta-agtaatcttgaagttttggaaagaaaacctcaaataagttacctgtcattgtcacagAGGTGTCGAGCTGGATGGTAACAGGGGAAAGACAGGCAACGCGGATTCGAGGATTGTACTTGAAAACAATATTGAGACAGGACATAGCATTCTTTGACAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccaacaataatttcagcattctgatatgagggttgttttattggatgttgcagAGGTATCATGTTGGATGATGACAGGAGAAAGACAAGCAGCAAGGATCCGTGGCTTGTACTTGAAAACTATATTGAAGCAGGACATTACCTTCTTTGACAC
ttctgat putative branch site (score: 3)
acaataattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acacgcacacttttgttatctttatttgcctggaactttgtagttttccaacaataatttcagcattctgatatgagggttgttttattggatgttgcagAGGTATCATGTTGGATGATGACAGGAGAAAGACAAGCAGCAAGGATCCGTGGCTTGTACTTGAAAACTATATTGAAGCAGGACATTACCTTCTTTGACAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
-cacgcac
- - - - - - - - - - - - - tgcctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggttgt