Sequence
atgc intronic sequence ATGC exonic sequencegtaatatgtgtttgctttgtgattttatatctttttccggcttttattttatggttcatttacttaccatgactctttaccggccttaaagTGTCAAGCAGGTGAATTTTTATGATGATGATGTACGCTTTTGGCAACTTTGGCATAACCGCTCTGCCGCTGCTGAGGCTCCAACAGCTGTCCATACTTCA
Basic information
species | Glycine max |
transcript | GLYMA03G38530.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G38530.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g46510.1 (Oryza sativa), 3'ss of exon 3
gtaatatgtgtttgctttgtgattttatatctttttccggcttttat-tttatggt-tcatttacttacca--tgactctttaccggccttaaagTGTCAAGCAGGTGAATTTTTATGATGATGATGTACGCTTTTGGCAACTTTGGCATAACCGCTCTGCCGCTGCTGAGGCTCCAACAGCTGTCCATACTTCA
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-------gtatt-gatttgtgttttttttccttctctggttctccatattcatggtatcatctgactcccaaatggttcactgtccttccccaagTGTAAAGCAGGTTAGCTTTTATGATGATGATGTTCGCTTTTGGCAACATTGGCGCAATTGCTCTGCTGCTGCTGAGGCTCCAACTGCGGTCAATCAACAA
upper sequence: GLYMA03G38530.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G000177_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------gtaatatgtgtttgctttgtgatt-ttatatctttttccggct---tttattttatggttcatttacttaccatgactct-ttaccggccttaaagTGTCAAGCAGGTGAATTTTTATGATGATGATGTACGCTTTTGGCAACTTTGGCATAACCGCTCTGCCGCTGCTGAGGCTCCAACAGCTGTCCATACTTCA
| | | |||||||| || || | || | | | || ||| | | ||| | ||| ||| | || |||||| |||||||| ||||||||||||||||| ||||||||||||| ||||| || | ||||| ||||||||||| ||||| || ||| || |
gtatgtcccttaattatgatgatcatgctaccctaacttgcttgggacttaaatgctttgttgttattgttaattatgatgatcatgtgcatattaccttcacctgactcccgatgggtctactgttcttctccaagTGTAAAGCAGGTTTCCTTTTATGATGATGATGTTCGCTTTTGGCAACATTGGCGCAATTGTTCTGCTGCTGCTGAGGCCCCAACTGCAGTCAATCAGCAA
upper sequence: GLYMA03G38530.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G24710.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatatgtgtttgctttgtgattttatatctttttccggcttttattttatggttcatttacttaccatgactctttaccggccttaaagTGTCAAGCAGGTGAATTTTTATGATGATGATGTACGCTTTTGGCAACTTTGGCATAACCGCTCTGCCGCTGCTGAGGCTCCAACAGCTGTCCATACTTCA
||| || | | || | | || || || | |||| | | | | ||||| | | | | ||| || || ||||||||||| |||||||| |||||||| || | ||||||||| |||| |||||||| || |||||||| ||||| |||||||| || |
gtagtagatagatctttctcgctgcta-attcagttgctcctttcgataatgagaaaaatgacttatctgctcaatgtttgcacctactagCGTTAAGCAGGTGAAGTTTTATGACGATGATGTGCGTTATTGGCAACTGTGGCGCAACCGCTCCGCAGCTGCTGAATCTCCATCAGCTGTCAATCATCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccggcttttattttatggttcatttacttaccatgactctttaccggccttaaagTGTCAAGCAGGTGAATTTTTATGATGATGATGTACGCTTTTGGCAACTTTGGCATAACCGCTCTGCCGCTGCTGAGGCTCCAACAGCTGTCCATACTTCA
tacttac putative branch site (score: 1)
ttttattttatggttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatgtgtttgctttgtgattttatatctttttccggcttttattttatggttcatttacttaccatgactctttaccggccttaaagTGTCAAGCAGGTGAATTTTTATGATGATGATGTACGCTTTTGGCAACTTTGGCATAACCGCTCTGCCGCTGCTGAGGCTCCAACAGCTGTCCATACTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG