Sequence
atgc intronic sequence ATGC exonic sequence...gaattgttcttgaataaaggtgcataacctctatggaagatttcatatgccactgatggatgcattttaaggtatcttgtatgtttttgttgtatttcagGTCAATTGTGTTGTAATGCGTGGATTTAATGATGATGAAATCTGTGACTTTGTTGAGTTGACGCGTGAAAAGCCAATTGATATTCGGTTTATAGAGTTCA
Basic information
species | Glycine max |
transcript | GLYMA08G16780.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G16780.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g32230.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------gaattgttcttgaataaaggtgcataacctctatggaagatttcatatgccactgatggatgcattttaaggtatcttgtatgtttttgttgtatttcagGTCAATTGTGTTGTAATGCGTGGATTTAATGATGATGAAATCTGTGACTTTGTTGAGTTGACGCGTGAAAAGCCAATTGATATTCGGTTTATAGAGTTCA
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gtatgcacattttcgtatatgtaaaatttctgcagtttgccttctttccaacattcctcaaagtggagctatatccac-atcataatgagcgtttatcattagttta---atttaattggttctctttccctttttctgc-tgccagGTCAACTGTGTTGTCATGCGTGGAATGAATGATGATGAGATCTGTGATTTTGTTGAAATGACGAGAGACAAGCCTGTCAATGTCAGATTTATTGAGTTTA
upper sequence: GLYMA08G16780.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G31955.1 (Arabidopsis thaliana), 3'ss of exon 2
gaattgttcttgaataaaggtgcataacctctatggaagatttcatatgccactgatggatgcattttaaggtatcttgtatgtttttgttgtattt--cagGTCAATTGTGTTGTAATGCGTGGATTTAATGATGATGAAATCTGTGACTTTGTTGAGTTGACGCGTGAAAAGCCAATTGATATTCGGTTTATAGAGTTCA
|||| | ||| | ||| ||| | | || | | | | | |||| || ||| | ||| | | || ||| ||| ||||||||||||||| | ||| | ||||| ||||||||||| || ||||| |||||||||||||| || || |||||||| || | ||||| || ||||| |
-gtatgtttattaatccttcttcatgttttctgtttga-atgtagcagaacgatatttgatg---ttcaagagtttttgcaaatcgttcttggttttgacagGTCAATTGTGTTATCATGAGGGGATTGAATGATGATGAGATTTGTGATTTTGTTGAGTTGACACGCGACAAGCCAATCAATGTCCGGTTCATCGAGTTTA
upper sequence: GLYMA08G16780.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0156g00170.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------------------------------gaattgttcttgaataaaggtgcataacctctatggaagatttcatatgccact-gatggatgcattttaaggtatcttgtatgtttttgttgtatttcagGTCAATTGTGTTGTAATGCGTGGATTTAATGATGATGAAATCTGTGACTTTGTTGAGTTGACGCGTGAAAAGCCAATTGATATTCGGTTTATAGAGTTCA
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gtatgttttgtcttttcaatttatgattgcatgcctttccttgctaaaatctgttcttttagatagtttctctttctgccaaagtaatattaggtcttattcattaggtcttattcattgtcttttataatgcaagattaaaacatattttccttccattcat-tctgtacgctgtctcagGTGAACTGTGTTGTAATGCGTGGGTTCAATGATGATGAGATCTGTGATTTCGTAGAGATGACTCGTGATAAACCAATTAATATTCGGTTTATTGAGTTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgccactgatggatgcattttaaggtatcttgtatgtttttgttgtatttcagGTCAATTGTGTTGTAATGCGTGGATTTAATGATGATGAAATCTGTGACTTTGTTGAGTTGACGCGTGAAAAGCCAATTGATATTCGGTTTATAGAGTTCA
cactgat putative branch site (score: 3)
tttttgtt putative PPT
tttttgttgtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaattgttcttgaataaaggtgcataacctctatggaagatttcatatgccactgatggatgcattttaaggtatcttgtatgtttttgttgtatttcagGTCAATTGTGTTGTAATGCGTGGATTTAATGATGATGAAATCTGTGACTTTGTTGAGTTGACGCGTGAAAAGCCAATTGATATTCGGTTTATAGAGTTCA
- - -gttcttg
- - - - - - - - - - tgcataa
- - - - - - - - - - - - - - - - - - - - - - - -tgccact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatgca