Sequence
atgc intronic sequence ATGC exonic sequencegtatacagaaaatttattatctctttccttattttttacttaaaggatttatgcacttaggaactcacttctgttgtggatttcagTTACGTGGCACCAGAATATGCTAACAGTGGTTTGTTAAATGAGAAGAGTGACATTTACAGCTTTGGTGTCCTCTTACTGGAAGCAGTTACTGGAAGGGAT
Basic information
species | Glycine max |
transcript | GLYMA02G45540.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g35450.1 (Oryza sativa), 3'ss of exon 5
------------------------------------------------------------------------------gtatacagaaaatttattatctct----ttccttattttttacttaaaggatttatgcacttaggaa-ctcacttctgttgtggatt----tcagTTACGTGGCACCAGAATATGCTAACAGTGGTTTGTTAAATGAGAAGAGTGACATTTACAGCTTTGGTGTCCTCTTACTGGAAGCAGTTACTGGAAGGGAT
||| || | ||| || || | | | | ||| | ||| ||| || ||| |||| | || | | |||| |||| || ||||| || || ||||| |||| ||| ||||||| ||||||||||| | ||||| |||||||| || |||||||||||||| ||||| || |||
gtatgttgatatttttttggagttagtattaatctttcctatgcttagcttttactgttggaatgtgcagtacttcgcttattcatacaatataaaattttacatgctgcgaactttgtccttcgtatattataacaggtagctttctcattgctatcattgattcatttcagGTATGTGGCCCCTGAGTATGCCAACACAGGTCTGTTAAACGAGAAGAGTGATGTCTACAGTTTTGGTGTGCTATTACTGGAAGCAGTGACTGGTAGAGAT
upper sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G026301_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------------------------------------------gtatacagaaaatttattatctctttccttattttttacttaaaggatttatgcactt-------------aggaac---tcac-ttctgttgtgg--atttcagTTACGTGGCACCAGAATATGCTAACAGTGGTTTGTTAAATGAGAAGAGTGACATTTACAGCTTTGGTGTCCTCTTACTGGAAGCAGTTACTGGAAGGGAT
|| || || | | || | || ||||| || | ||| | |||| |||| || ||||| |||||| || ||||| || |||||||| |||| |||| |||||||||||| |||||| | ||||| ||||| || || |||||||| |||||||||| |||||
gtatgttgtttgcttgatattctttcatttttgtagtaccttgcttgactaactggaacatgtggtattacagtaggaacctttacatgttgagggatttgtttttcatgtttttagagcagtataaagttttgtggtgcttcacatgacatgaaaagaaccattcaccttttgttgctactgtttcagGTATGTGGCCCCTGAATATGCCAACACTGGTCTGTTAAATGAGAGGAGTGATGTCTACAGTTTTGGAGTGCTACTACTGGAATCAGTTACTGGGAGGGAC
upper sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G017386_T03 (Zea mays), 3'ss of exon 5
---------gtatacagaaaatttattatctctttccttattttttacttaaaggatttatgcacttagga---actcacttctgttgtggatttcagTTACGTGGCACCAGAATATGCTAACAGTGGTTTGTTAAATGAGAAGAGTGACATTTACAGCTTTGGTGTCCTCTTACTGGAAGCAGTTACTGGAAGGGAT
| | || || ||| || | | | | | || || |||| | || |||| | || ||||| || || ||||| ||||||||||| | ||| |||||||||| ||||||||| ||||||| ||||| || ||||| | ||| | || || |||||| ||
gtattattcttttttctaacccatacctgctcatttgctttgtgtctttacaatgacttatagagtttaactttcctcatccatttttcttgcttcagATATGTTGCACCTGAATATGCTAATACTGGAATGTTAAATGAAAAGAGTGACGTTTACAGTTTTGGCGTTCTCTTGTTAGAAACTGTGACAGGAAGGAAT
upper sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatacagaaaatttattatctctttccttattttttacttaaaggatttatgcac-ttaggaactcacttctgttgtggatttcagTTACGTGGCACCAGAATATGCTAACAGTGGTTTGTTAAATGAGAAGAGTGACATTTACAGCTTTGGTGTCCTCTTACTGGAAGCAGTTACTGGAAGGGAT
||| ||||||| | |||||| | || | || | ||| || ||| ||| | | ||| | |||| || || ||||| ||||||||||| | ||| | || ||||||||||||||||| || |||||||||||||| | || || | | |||||||| |||
gtaagtctaaaatttgtaccctctttggtgatgatgggttt-----ttgtatacatattattaacggtcatgtgt-atatgcatcagATATGTCGCACCCGAATATGCTAATACAGGTCTATTGAATGAGAAGAGTGACATCTATAGCTTTGGTGTCCTGCTGCTAGAGACTATAACTGGAAGAGAT
upper sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 6
---------------------gtatacagaaaatttattatc-tctttccttattttttacttaaaggatttatgca---cttaggaactcacttctgttgt--ggatttcagTTACGTGGCACCAGAATATGCTAACAGTGGTTTGTTAAATGAGAAGAGTGACATTTACAGCTTTGGTGTCCTCTTACTGGAAGCAGTTACTGGAAGGGAT
| | | | |||| | ||||| | | | | |||| |||||| || || | || || ||| || | |||||||||||| |||||||||||||||||||| | ||| |||||||||||||||||||| || |||||||||||||| ||| | ||||||||||||||||||||||||
gtatgtttatatgttcatcttaagtcccctttagtctttatagtttttccacctgtatgatataaattttttatgagagcctcagaacctgacatcttttctctggatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttacttaaaggatttatgcacttaggaactcacttctgttgtggatttcagTTACGTGGCACCAGAATATGCTAACAGTGGTTTGTTAAATGAGAAGAGTGACATTTACAGCTTTGGTGTCCTCTTACTGGAAGCAGTTACTGGAAGGGAT
aactcac putative branch site (score: 2)
tacttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatacagaaaatttattatctctttccttattttttacttaaaggatttatgcacttaggaactcacttctgttgtggatttcagTTACGTGGCACCAGAATATGCTAACAGTGGTTTGTTAAATGAGAAGAGTGACATTTACAGCTTTGGTGTCCTCTTACTGGAAGCAGTTACTGGAAGGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG