Sequence
atgc intronic sequence ATGC exonic sequence...ttttgtatgtgaagttgcattctttgagttaaaaatttctggtcgatatatcttatacctgctactagatattaattttcttttcatcaattcatgacagATATCAGATGGATGTCAATGGAGAAAGTATGGACAGAAGATGGCAAAAGGGAATCCATGTCCGCGATCTTATTATCGTTGCTCAATGGGGACTGCTTGTC
Basic information
species | Glycine max |
transcript | GLYMA08G43260.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G43260.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G62300.1 (Arabidopsis thaliana), 3'ss of exon 4
ttttgtatgtgaagttgc---attctttgagttaaaaatttctggtcgatatatcttatacctgctactagatattaattttcttttca--tcaattcatgacagATATCAGATGGATGTCAATGGAGAAAGTATGGACAGAAGATGGCAAAAGGGAATCCATGTCCGCGATCTTATTATCGTTGCTCAATGGGGACTGCTTGTC
||| || | || || || | ||| || | | | ||| ||| |||| |||| ||||||| ||||| | | | | | ||||| |||||||||||||||||||| ||||| ||||||||||| ||||||||||| |||||||| | ||||| || ||| | |||| || | ||||
----gtaagttgatttattagatactaatacttataagactatataaaaaataaactatg--tgct-ttagagattaattatctttgtactttatgtttctatagATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGGAATCCTTGTCCGCGGGCATATTACCGCTGCACGATGGCCACGGGCTGTC
upper sequence: GLYMA08G43260.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0090g00840.t01 (Vitis vinifera), 3'ss of exon 4
ttttgtatgtgaagttgcattctttg--agttaaaaatttctggtcgatatatcttatacctgc-tactagatattaattttcttttcatcaattcatgacagATATCAGATGGATGTCAATGGAGAAAGTATGGACAGAAGATGGCAAAAGGGAATCCATGTCCGCGATCTTATTATCGTTGCTCAATGGGGACTGCTTGTC
||| || || || | | |||| || || ||| | | | || || | | | | || | | || ||| | | || |||||| || |||||||| |||||||||||||||||||| |||||||| ||||| || ||||| || ||| |||||||||| ||| | |||| ||||||||||
-tttcaatcacaatctggactgtttgtagattggaagattcagtactccaaattataaaaataaatgtttgaccattggccgatcttaatccact-at-acagATCTCCGATGGATGCCAATGGAGAAAGTATGGACAAAAGATGGCGAAAGGAAACCCATGCCCTCGAGCTTATTATCGATGCACCATGGCAACTGCTTGTC
upper sequence: GLYMA08G43260.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S246_89V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------ttttgtatgtgaa--gttgcattctttgagttaaaaatttctggtcgatat-atcttatacctgctactagatattaattttcttttcatcaattcatgaca----gATATCAGAT-------GGATGTCAATGGAGAAAGTATGGACAGAAGATGGCAAAAGGGAATCCATGTCCGCGATCTTATTATCGTTGCTCAATGGGGACTGCTTGTC
|| || | || | | | || | | || | | || | | ||| | | | | || | | | | | | || || | | | |||||| ||||| || |||||||| ||||| ||||||||||| ||||||||||| || || || | ||||| || ||| | | | ||| ||||
gtgagaacttggagttctttaaatacttcaacagctactctcatcgcattgcttttgtagcttcaaagccagctttaagcagttgatatgtgtaagtccctggattaacatggtgagatattttgttttcagATTAACGACGGATGCCAGTGGAGAAAATATGGTCAGAAGATGGCTAAAGGGAATCCTTGCCCTCGCGCATATTACCGCTGCACTGTTATGTCTGGCTGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatatcttatacctgctactagatattaattttcttttcatcaattcatgacagATATCAGATGGATGTCAATGGAGAAAGTATGGACAGAAGATGGCAAAAGGGAATCCATGTCCGCGATCTTATTATCGTTGCTCAATGGGGACTGCTTGTC
tattaat putative branch site (score: 2)
tagatattaattttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttgtatgtgaagttgcattctttgagttaaaaatttctggtcgatatatcttatacctgctactagatattaattttcttttcatcaattcatgacagATATCAGATGGATGTCAATGGAGAAAGTATGGACAGAAGATGGCAAAAGGGAATCCATGTCCGCGATCTTATTATCGTTGCTCAATGGGGACTGCTTGTC
- -tgtatgt
- - - - - - - - gcattct
- - - - - - - - - - - - - - - - - -tttctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctac