Sequence
atgc intronic sequence ATGC exonic sequencegtaattcattattcgtccttttttttttttgcaatagattaggggttctgttttgacattgatcagcatctctaatgctctgccagACGACAAGACTCATCAATTGGTTTTGGAGCTCCTGTTCGTGCCAACATGGCTACCAGTGGAGTGACCAGTGGTGCAATAACTTCATCTTTGCTAGAATCG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G33360.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G32040.1 (Glycine max), 3'ss of exon 7
gtaattcattattcgtccttt-----tttttttttgcaatagattaggggttctgttttgac---attgatcagcat-ctctaatgctctg---------ccagACGACAAGACTCATCAATTGGTTTTGGAGCTCCTGTTCGTGCCAACATGGCTACCAGTGGAGTGACCAGTGGTGCAATAACTTCATCTTTGCTAGAATCG
||| || || || ||| | | | |||||| ||| | | | | || ||| | ||| ||| || | | || | || ||||||||||||| || ||||||||||||||||| ||||| ||| |||| ||| | ||||| | || | || |||| | || |||||||| || || |||
gtattttttt-tttgtcttgtaagaatgttttttcacaaatgttctgcattcttggttttgctagatttttcatcaaattttgattatttgtgaaataaaccagACGACAAGATTCTTCAATTGGTTTTGGAGCACCTGTCCGTTCCAATATGAGAGCTGGTGGAATTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCG
upper sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 10
----------------------gtaattcattattcgtccttttt--tttttttgcaatagattaggggttctgttttgacattgatcagcatctctaatgctctgccagACGACAAGACTCATCAATTGGTTTTGGAGCTCCTGTTCGTGCCAACATGGCTACCAGTGGAGTGACCAGTGGTGCAATAACTTCATCTTTGCTAGAATCG
|| | || || | | || ||| || || | || ||||| | | | | || | | | | ||||||||||||| || || |||||||||||||| || ||||||||||| ||| | ||||| | || | |||| |||| |||||||| || || ||
gtaatgttggcctttgtcttgcaaaaatatttgctcataaatcacagttggtttacatatgacttggt-ttctgctgtactaacttatacgatttatcaaa-taaaccagACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAGAGCTGGTGGAATAACAGATTCTGCAGTAACATCATCTTTACTTGAGTCA
upper sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G28260.1 (Glycine max), 3'ss of exon 10
------------------------gtaattcattattcgtccttttttttttttgca-atagattaggggttctgttttgacattgatcagcatct-ctaatgctctg-----ccagACGACAAGACTCATCAATTGGTTTTGGAGCTCCTGTTCGTGCCAACATGGCTACCAGTGGAGTGACCAGTGGTGCAATAACTTCATCTTTGCTAGAATCG
|| | || || | | || | | ||| | || |||||| ||| | | | | | ||| | || ||||||||||||| || || |||||||||||||| || |||||||| || ||| | |||| | || | |||| |||| |||||||| || || ||
gtaaaatgttggccttcggcttgcaaaaatatttgctcataaatcacagttggtttacatatgtcttggtttctgtcggagtattcactaacttgtactatttatcaaataaaccagACGACAAGATTCTTCTATTGGTTTTGGAGCCCCAGTTCGTGCAAATATGAGAGCTGTTGGAATAACAGATTCTGCAGTAACATCATCTTTACTTGAGTCA
upper sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 9
gtaattcattattcgtccttttttttttttgcaatagatt---aggggt--tctgttt---tgacattgatca------gcatctcta-atg----ctctgccagACGACAAGACTCATCAATTGGTTTTGGAGCTCCTGTTCGTGCCAACATGGCTACCAGTGGAGTGACCAGTGGTGCAATAACTTCATCTTTGCTAGAATCG
| | | || | | | | | || || ||| || ||| | | ||| | | || | | | | | ||| ||| | | ||||||| ||||| || ||||||||||||||||| ||||||||||| |||||| || |||| | |||| || || | || ||||| || |||||||||
-----tgtgtgtgtgtgtgtgtgtgtgtgtgaaagagagagagagaggtaatatatttgaataatatggcctaaactttggaaccctacatggtttttttaccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG
upper sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 10
---------------------------------------gtaattcattattcgtccttttttttttttgcaatagattaggg-gttct---gttttgacattgatcagcatctctaatgctctgccagACGACAAGACTCATCAATTGGTTTTGGAGCTCCTGTTCGTGCCAACATGGCTACCAGTGGAGTGACCAGTGGTGCAATAACTTCATCTTTGCTAGAATCG
| | ||||| ||| | | || ||||| || || | ||| | | | ||| | | || | | | ||| ||||| |||||||||||||||||||| |||||||||||||| ||| | | ||| | | || || |||||||||||||| || ||
gtaggcttcttcatcttcaagtgttaaggtcaacgaatagcatttcatgatttatttgtcttctttttgataactttttgttgtgttatcaaaccctcatgcctttcaacct-tcgtttcttgtttcagGAAGCAAGATTCATCAATTGGTTTTGGAGCACCTGTTCGTGCCAATATGCGAGGAAACAAACTGATCGACGCCGCCATTACTTCATCTTTGCTTGAGACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatagattaggggttctgttttgacattgatcagcatctctaatgctctgccagACGACAAGACTCATCAATTGGTTTTGGAGCTCCTGTTCGTGCCAACATGGCTACCAGTGGAGTGACCAGTGGTGCAATAACTTCATCTTTGCTAGAATCG
ctctaat putative branch site (score: 3)
ctctgcc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattcattattcgtccttttttttttttgcaatagattaggggttctgttttgacattgatcagcatctctaatgctctgccagACGACAAGACTCATCAATTGGTTTTGGAGCTCCTGTTCGTGCCAACATGGCTACCAGTGGAGTGACCAGTGGTGCAATAACTTCATCTTTGCTAGAATCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG