Sequence
atgc intronic sequence ATGC exonic sequencegttttttattcgtcatctttcattaacatcgatgtactgttggttgctttatgagtatctaatttatctttttctaccatatagGCGCTTGTTGTCCTGGTGCATGATATGGGCCCTAACTGGGAGCTCATTAGTGATGCAATGAACAGCACTCTTAAAATTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G24880.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G24880.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA16G14060.1 (Glycine max), 3'ss of exon 17
------------------------gttttttattcgtcatctttcattaa-cat----cgatgtactgttggttgctt-tatgagtatctaatttatctttttctacc--atatagGCGCTTGTTGTCCTGGTGCATGATATGGGCCCTAACTGGGAGCTCATTAGTGATGCAATGAACAGCACTCTTAAAATTAAG
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gttgtttggaattcatttgctttatcattttttgtgttattttttaataaatattttacactttaatatctatcaattgtgtaaaagacttaccattattctcctgcctgttgcagGCTCTTGTGGTCCTGGTGCATGATATGGGTCCAAACTGGGAGCTCATAAGTGATGCTATCAATAGTGCTCTTCAAATTAAG
upper sequence: AT3G24880.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA08G46710.1 (Glycine max), 3'ss of exon 18
---------------------------gttttttattcgtcatctttcattaacatcgatgtactgttggttgctttatgagtatctaatttatctttttctaccatatagGCGCTTGTTGTCCTGGTGCATGATATGGGCCCTAACTGGGAGCTCATTAGTGATGCAATGAACAGCACTCTTAAAATTAAG
|| | ||||| ||| | | || | || || ||| | | | | | | || | | | | |||| |||||||||||||||||||||||||| || ||||||||||| |||||||||| || ||||| ||| | || | |||
gttgtctgttgttcgatagttatctcaacttaactcttgtcatgttttgg-agtaaatatttgaacttagtgactt-acagaaagttgttatctattatccaatgttgcagGCTCTTGTTGTCCTGGTGCATGATATGGGTCCAAACTGGGAGCTTGTTAGTGATGCTATCAACAGTACTATACAATTCAAG
upper sequence: AT3G24880.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA18G36660.1 (Glycine max), 3'ss of exon 15
-------gttttttattcgtcatctttcattaacatcgatgta--ctgttgg-----------ttgctttatgagt------atctaatt-tatctttttctaccatatagGCGCTTGTTGTCCTGGTGCATGATATGGGCCCTAACTGGGAGCTCATTAGTGATGCAATGAACAGCACTCTTAAAATTAAG
||| ||| || || |||| ||||| | |||| | |||| ||| |||| | | || || | | || | | | | |||| |||||||||||||||||||||||||| || ||||||||||| ||| |||||| || ||||| ||| | || | |||
gttgtttgttgtttgttagttatctcaacttaacttttatgttgttttttggagtaaatatttcaacttcatgacttgcataaactggttatctattatccaatgttgcagGCTCTTGTTGTCCTGGTGCATGATATGGGTCCGAACTGGGAGCTTGTTAATGATGCCATCAACAGTACTATACAATTCAAG
upper sequence: AT3G24880.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA03G18730.1 (Glycine max), 3'ss of exon 6
--------------------------gttttttattcgtcatctttcattaacatcgatgt-----actgttggttgcttta--tgagtatctaatttatc----tttttctacca--tatagGCGCTTGTTGTCCTGGTGCATGATATGGGCCCTAACTGGGAGCTCATTAGTGATGCAATGAACAGCACTCTTAAAATTAAG
|||||| | || || || | | || || | ||| | | | | || ||| ||| | || | || || | |||| ||||| || ||||||||||||||||| || |||||||||||| | |||||||| || || || |||| |||| |||
gttgtttggaattcatttgctttatcattttttctctgttattattgaattgaataaatattttacactttaaaatctatcaattgtgtaaagggcttaccattattctcctgcctgttgcagGCTCTTGTGGTGCTGGTGCATGATATGGGTCCAAACTGGGAGCTCGTAAGTGATGCTATCAATAGTGCTCTCCAAATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgatgtactgttggttgctttatgagtatctaatttatctttttctaccatatagGCGCTTGTTGTCCTGGTGCATGATATGGGCCCTAACTGGGAGCTCATTAGTGATGCAATGAACAGCACTCTTAAAATTAAG
atctaat putative branch site (score: 3)
tttatctttttctacc CT-rich tract
tatctaatttatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttttattcgtcatctttcattaacatcgatgtactgttggttgctttatgagtatctaatttatctttttctaccatatagGCGCTTGTTGTCCTGGTGCATGATATGGGCCCTAACTGGGAGCTCATTAGTGATGCAATGAACAGCACTCTTAAAATTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA