Sequence
atgc intronic sequence ATGC exonic sequence...cattctttctttgttatgattatataatgtagcaacctgatttttgctgtgttttctcagttattatattttgtatgttgactcttttatctgtaaacagCGTTTTGCTGCAGTAATCATGAGAATAAGAGAACCCAAAACCACGGCACTGATATTTGCATCGGGTAAAATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 2
cattctttctttgttatgattatataatgt--agcaacctgatttttgctg---tgttttctcagttat-tatatttt-gtatgttgactcttttatctgtaaacagCGTTTTGCTGCAGTAATCATGAGAATAAGAGAACCCAAAACCACGGCACTGATATTTGCATCGGGTAAAATG
| | | ||||| || | | | || || | | | | | | || || ||| |||| || || | |||| | | | |||||||||||||||||||| |||||||||||||||||||| ||||| || || ||||||||||||||||||||||||
-------tgcacactgaggttatagcatctctatctactccatccgttccaaaatataagcactgtaatatatgttttagtttgctaactcctcttttcacaaacagCGTTTTGCTGCAGTTATCATGAGAATAAGAGAACCGAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
cattctttctttgttatg-attatat-aatgtagcaacctgatttttgctgtgttttctcagttatt-atatttt-gtatgttgactcttttatctgtaaacagCGTTTTGCTGCAGTAATCATGAGAATAAGAGAACCCAAAACCACGGCACTGATATTTGCATCGGGTAAAATG
||| ||| | | | ||| | | || ||| | ||| | || | || ||| || |||| || || | | || | | |||||||||||||||||| || |||||||||||||||||||| ||||| || || ||||||||||||||||||||||||
----cttagattgatttacactatgtcagtggcgcactatataatttcatactcatttgctgtaatttatgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 3
cattct-ttctttgttatgattatataatgtagcaacctgatttttgctgtgttttctcagttattatattttgta-tgttgactct--tttatctgtaaacagCGTTTTGCTGCAGTAATCATGAGAATAAGAGAACCCAAAACCACGGCACTGATATTTGCATCGGGTAAAATG
|||| || || | || |||| | || || | |||| |||| | | | | | ||| |||| || || || | | | | || |||||||||||||| || || ||||| |||||||| |||||||| || ||||| || ||||| || || || |||
--ttctgttattcggaatcattaatt--tgcagatgtattatttgtgctagttctaatggttggtggtatgctgtactgatgtctgtgatgtgtttggttgcagCGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTTATTTTTGCTTCTGGCAAGATG
upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
------cattctttctttgttatgattatataatgtagcaacctgatttttgctgtgttttctcagttattatattttgtatgttgactcttttatctgtaaacagCGTTTTGCTGCAGTAATCATGAGAATAAGAGAACCCAAAACCACGGCACTGATATTTGCATCGGGTAAAATG
||| | | ||||| ||| | | | | ||| || | | || ||||| || | | ||||| || | | | | || | |||||||||||||| ||||||||||| ||||| || || ||||||||||| |||||||||| || || || |||
gatcaacatcttaaccttgttcctattgga----ggaattttttttctttccctatttgttgccagttttttt--tatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 2
lower sequence: EFJ29072 (Selaginella moellendorffii), 3'ss of exon 2
cattctttctttgttatgattatataatgtagcaacctgatttttgctgtgttttctcagttattatattttgtatgttgactcttttatctgtaaac-agCGTTTTGCTGCAGTAATCATGAGAATAAGAGAACCCAAAACCACGGCACTGATATTTGCATCGGGTAAAATG
| ||| || | | |||| | | || | |||| | ||| |||| | ||| | | | ||||||||||||| || |||||| | ||||||||||||||||||||||| || || ||||| || || || |||
-----------------------------------gtttgtttgtgttcttttttttt--ctcttgtgttttatgacttgtctctctcttctcttatccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG
upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 2
lower sequence: EFJ17606 (Selaginella moellendorffii), 3'ss of exon 2
cattctttctttgttatgattatataatgtagcaacctgatttt-tgctgtgttttctca-gttattatattttgtatgttgactcttttatctgtaaacagCGTTTTGCTGCAGTAATCATGAGAATAAGAGAACCCAAAACCACGGCACTGATATTTGCATCGGGTAAAATG
|| || | | || | ||||||| ||| |||| |||| | | |||| || ||| || |||||||||||||| || |||||| | ||||||||||||||||||||||| || || ||||| || || || |||
----------------------------------gtttgtttgtgttcttttttttctcttgtttttatgacttgtctctct-ctctcttctct-tatccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctgtgttttctcagttattatattttgtatgttgactcttttatctgtaaacagCGTTTTGCTGCAGTAATCATGAGAATAAGAGAACCCAAAACCACGGCACTGATATTTGCATCGGGTAAAATG
tgttgac putative branch site (score: 3)
ctcttttatct CT-rich tract
ttttctcagttattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattctttctttgttatgattatataatgtagcaacctgatttttgctgtgttttctcagttattatattttgtatgttgactcttttatctgtaaacagCGTTTTGCTGCAGTAATCATGAGAATAAGAGAACCCAAAACCACGGCACTGATATTTGCATCGGGTAAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA