Sequence
atgc intronic sequence ATGC exonic sequence...atttatttaatgccatgtatcaagatgcgatagcttgctgtggtttactctaatggcaggtctatttagcagtgctgaaagtattttgtttacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
Basic information
species | Glycine max |
transcript | GLYMA08G13310.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G13310.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g34680.1 (Oryza sativa), 3'ss of exon 3
atttatttaatgccatgtatcaaga-tgcgatagcttgctgtggtttactctaatggcaggtctatttagcagt--gctgaaagtattttgttt---------acattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
|| | || || | || | |||| | || | | ||| | ||| | || | | || ||| | |||||| ||| || |||||||||||| | || ||||| ||| |||| || |||||||| ||||||||||| |||| | | ||||| || ||||||||||||||||| |||
--gtactgcctgtaatctttcttgcctgcgttggcct-ttctggatcactatggcattgctgcttctgggttgttcgctaatgttattttctttttgaatctgactttgcagAAATTTTTAGACAGCTCTAAGCTGAAGAGGCATTTTCTTATTCATACAGGAGAGAAGAACTTTGTCTGCCCTCATGAAGGCTGTGGAAAG
upper sequence: GLYMA08G13310.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G885700_T02 (Zea mays), 3'ss of exon 3
--------atttatttaatgccatgtatcaagatg--cgatagcttgctgtggtttactctaatggcaggtctatttagcagtgctgaaagtattttgttt-acattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
| ||| | || | || | | || ||| || | | || ||| | || | | | || | | | | | ||||||||||| | ||||| || |||||||| ||||||||||| ||||||||||| || | | |||||||||| || |||||||| ||||| |||
gtactgtttataattcctggtcacatcccagagtaatcttcagtctgcaaaggcatgtttctatttcagttgc-ttgattaatcctttttctgctaaatctgattttgcagAAATTCTTAGATAGTTCTAAGTTGAAGAGACATTTTCTTATTCATACAGGAGAAAAGAATTTTGTGTGCCCACATGAAGGTTGTGGGAAG
upper sequence: GLYMA08G13310.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G140016_T01 (Zea mays), 3'ss of exon 3
-----attta---tttaatgccatgtatcaagatg--cgatagcttgctgtggtttactctaatggcag--gtctatttagcagtgctgaaagtattttgtttacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
|||| || | || | || | | || ||| || | || || ||| | | || | | ||| || | | ||||||||||| | |||||||| |||||||| ||||||||||| || ||||| || |||| | |||||||||| || |||||||| ||||| | |
gtactgtttacccttccttttcacatcccagagtaatcttcagtctgcaaaggcatggtcccatttcagttgcttgactaatcttttttcgggtaaatt--tgattttgcagAAATTCTTAGATAGCTCTAAGTTGAAGAGACATTTTCTTATCCATACTGGAGAGAAGAATTTTGTGTGCCCACATGAAGGTTGTGGGAGG
upper sequence: GLYMA08G13310.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G06634.3 (Arabidopsis thaliana), 3'ss of exon 3
atttatttaatgccatgtatcaagatgcgatagcttgctgtggtttactctaatggcaggtctatttagcagtgctgaaagtattttgtttacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
|||||| || || || | |||| | | ||| | ||| | | | ||| | || | ||| ||| | ||||||||||||||||| ||||||||||| ||||||| ||| |||||||| || ||||| ||| | | ||| || ||||||| ||||| |||
----gtttaataatat-cctctctttggtttggcttaca--cactcactttcatgatatattga---agccatcttg----tttttgttttttgtaacagAAATTTCTGGATAGTTCAAAGTTGAAGAGACATTATCTTATTCATACTGGAGAGAGAAATTATATATGTACTTATGAAGGATGTGGAAAG
upper sequence: GLYMA08G13310.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0035g00660.t01 (Vitis vinifera), 3'ss of exon 3
atttatt-taatgccatgtatcaagatgcgatagcttgctgtggtttactctaatggcaggtctatttagcagtgctgaaagtattttgt--ttacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
|| | | | || | | | | | | | || || |||| || ||||| | |||| | |||| ||| ||||||||||| ||||||| |||||| |||||||||| || || ||||||||||| ||||| ||||||||||||||||||||||||||||| |||
-cccataatgtttctattttccccacttttctctcatctaatttttctctgctccatcaggctgat--gacagtgttaaaagattcttgtatttatgatgcagAAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGAGAGAGAGATTTTGTGTGTCCTCATGAAGGCTGTGGGAAG
upper sequence: GLYMA08G13310.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S42_134V6.1 (Physcomitrella patens), 3'ss of exon 3
atttatttaatgccatgtatcaagatgcgatagcttgctgtggtttactctaatggcaggtctatttagc-----agtgctgaaagtattt--tgtttacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
| | | | || ||| || | || || | | | | || || || | | | ||| | |||| ||| ||| | ||| || | || ||||||||| |||||||||||||||| |||||||| ||||||| | ||||||| ||||| |||||||||||| |||
------tccttatctgttttctagacacgctttattattggaatatgtgttcttaccaagttctctttgtcatcaacttatgataacatttgatgtctacgt-acagCGTTTCGTCGACAGCTCAAAGCTGAAAAGACATTTTCTGATTCATACGGGGGAGAAGCATTTTGTTTGTCCATTTGAAGGCTGTGGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactctaatggcaggtctatttagcagtgctgaaagtattttgtttacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
ctctaat putative branch site (score: 3)
ttttgttt putative PPT
aaagtattttgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttatttaatgccatgtatcaagatgcgatagcttgctgtggtttactctaatggcaggtctatttagcagtgctgaaagtattttgtttacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - aatgcca
- - - - - - - - - - - - - - - - gcttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaggtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgaa