Sequence
atgc intronic sequence ATGC exonic sequence...aaatgttggattttttgttgtttgttgatagtgagtaaaatctacaacaaataagattactgatcgctacttctctatatattttttcatcctatttcagAAAGTATAAAGCTTTACATTTCTGACAACAAGGTGATCTTGACGGAAGGTTTTGATGGTGTTGTTCCTCCGAAGTATTTTGAAAGGATAGAATCATGGCC
Basic information
species | Glycine max |
transcript | GLYMA17G29450.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G29450.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g04300.1 (Oryza sativa), 3'ss of exon 6
aaatgttggattttttgttgtttgttgatagtgagtaaaatctacaacaaataagattactgatcgctacttctctatatattttttcatcctatttcagAAAGTATAAAGCTTTACATTTCTGACAACAAGGTGATCTTGACGGAAGGTTTTGATGGTGTTGTTCCTCCGAAGTATTTTGAAAGGATAGAATCATGGCC
| | | |||||| | | || | | | | | | || | || || ||| || ||| | | | | ||||| | || ||||| |||||||| |||||||||||||| |||| || ||||| ||||| ||||||||| |||||| || || | || ||| |||||||
--gtatgatgctgtttgtttatagccacaagcaatctatttattct-cttatcaacttgctaggggctggtttctgatagctgaatctgtt---tctcagATGGAATGAAGCTGTACATTTCAGACAACAAGGTGATTCTGACAGAGGGTTTCGATGGCGTTGTTCCTGTGAAGTACTTCGAGAAAATTGAAACATGGCC
upper sequence: GLYMA17G29450.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G061783_T04 (Zea mays), 3'ss of exon 4
aaatgttggattttttgttgtttgttgatagtgagtaaaatctacaacaaataagattactgatcgctacttctctatatattttttcatcctatttc--agAAAGTATAAAGCTTTACATTTCTGACAACAAGGTGATCTTGACGGAAGGTTTTGATGGTGTTGTTCCTCCGAAGTATTTTGAAAGGATAGAATCATGGCC
| | | | | || || |||| ||| | | | | || |||| |||| ||||| | | | || | || | || |||||||| ||||| |||||||| ||||||||||| |||||||||||||| || || || ||| || |||||||| | ||| |||||||
-------gtactatataatgcttacaaataggctcccaaa---aaatttctttcgttttctgagtgctagaggctaatataacacctaaatttgttgcgcagGTGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGATGGCGTCGTCCCGGTGAAATACTTTGAAAGAGTCGAAACATGGCC
upper sequence: GLYMA17G29450.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G092568_T02 (Zea mays), 3'ss of exon 4
aaatgttgg-attttttgttgtttgttgatagtgagtaaaatctacaacaaataagattactgatcgctacttctctatatattttttcatcctatttc--agAAAGTATAAAGCTTTACATTTCTGACAACAAGGTGATCTTGACGGAAGGT------TTTGATGGTGTTGTTCCTCCGAAGTATTTTGAAAGGATAGAATCATGGCC
| | || | | | | || || |||| ||| | || | | || |||| |||| ||||| | | | | | ||| | || |||||||| ||||| |||||||| ||||||||||| |||||| |||||||| ||||| ||| ||| || |||||||| || ||| |
acttaaaggtactatataatgcttacaaataggcccccaaa---aaaattctttcgttttctgagtgctagaggctgatataacacctaaatttgtcgcgcagATGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGGTTTTGATGGCGTTGTCCCTGTGAAATACTTTGAAAGAATCGAAAC------
upper sequence: GLYMA17G29450.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G092568_T01 (Zea mays), 3'ss of exon 7
aaatgttggattttttgttgtttgttgatagtgagtaaaatctacaacaaataagattactgatcgctacttctctatatattttttcatcctatttc--agAAAGTATAAAGCTTTACATTTCTGACAACAAGGTGATCTTGACGGAAGGTTT------TGATGGTGTTGTTCCTCCGAAGTATTTTGAAAGGATAGAATCATGGCC
| | | | | || || |||| ||| | || | | || |||| |||| ||||| | | | | | ||| | || |||||||| ||||| |||||||| ||||||||||| |||||||| |||||| ||||| ||| ||| || |||||||| || ||| |
-------gtactatataatgcttacaaataggcccccaaa---aaaattctttcgttttctgagtgctagaggctgatataacacctaaatttgtcgcgcagATGGGATGAAGCTTTATATTTCAGACAACAAAGTGATCTTGACAGAAGGTTTTGGTTTTGATGGCGTTGTCCCTGTGAAATACTTTGAAAGAATCGAAAC------
upper sequence: GLYMA17G29450.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv15s0048g00300.t01 (Vitis vinifera), 3'ss of exon 7
-----------------aaatg--ttggattttttgttgtttg--ttgatagtgagtaaaatctacaacaa-ataagat-tactgatcgctact-----tctctatatattttttcatcctatttcagAAAGTATAAAGCTTTACATTTCTGACAACAAGGTGATCTTGACGGAAGGTTTTGATGGTGTTGTTCCTCCGAAGTATTTTGAAAGGATAGAATCATGGCC
||||| |||| | | | | || | | ||| | || | |||| || ||| | || | ||||| | | | | | | || | ||| ||| | || ||||| |||||||| ||||||||||| |||||||| |||||||||||||||||||| ||| ||||| ||||||| ||||||||| |||||
gtatacccttaaattcaaaatgagttggtccaactcctataggagttcagaatgaatcctatttgtaacagtatgagagatgtagaacactactaatgcttttttccccgtctctaattcaattgtagATGGAATGAAGCTCTACATTTCAGACAACAAGGTCATCTTGACCGAAGGTTTTGATGGTGTTGTGCCTGTCAAGTACTTTGAAAAGATAGAATCTTGGCC
upper sequence: GLYMA17G29450.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv15s0048g00280.t01 (Vitis vinifera), 3'ss of exon 7
----------------------aaatgttggattttttgttgtttgttgatagtgagtaaaatctacaacaa-ataagat-tactgatcgctact----tctctatatattttttcatcctatttcagAAAGTATAAAGCTTTACATTTCTGACAACAAGGTGATCTTGACGGAAGGTTTTGATGGTGTTGTTCCTCCGAAGTATTTTGAAAGGATAGAATCATGGCC
|| || | | | | | | ||| | | ||| | |||| |||| |||||| | || | ||||| | | | | | || | ||| ||| | || ||||| |||||||| ||||||||||| |||||||| |||||||||||||||||||| ||| ||||| ||||||| ||||||||| |||||
gtatacctttaaattcaaaatgaattggtccaactcctatagga-gttcagaatgaatcctatctgtaacagtataagagatgtagaacactactaatgctttttccccgtctctaattcaattgtagATGGAATGAAGCTCTACATTTCAGACAACAAGGTCATCTTGACCGAAGGTTTTGATGGTGTTGTGCCTGTCAAGTACTTTGAAAAGATAGAATCTTGGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacaaataagattactgatcgctacttctctatatattttttcatcctatttcagAAAGTATAAAGCTTTACATTTCTGACAACAAGGTGATCTTGACGGAAGGTTTTGATGGTGTTGTTCCTCCGAAGTATTTTGAAAGGATAGAATCATGGCC
tactgat putative branch site (score: 2)
ttttttcatcctattt putative PPT
tatatattttttcatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatgttggattttttgttgtttgttgatagtgagtaaaatctacaacaaataagattactgatcgctacttctctatatattttttcatcctatttcagAAAGTATAAAGCTTTACATTTCTGACAACAAGGTGATCTTGACGGAAGGTTTTGATGGTGTTGTTCCTCCGAAGTATTTTGAAAGGATAGAATCATGGCC
- atgttgg
- - - - - - - - - tgtttgt
- - - - - - - - - - - - - gatagtg