Sequence
atgc intronic sequence ATGC exonic sequencegttcgatgttttcctctgttttcttcttccatctataacagatctgcagaaccgatccggttcaagatcatttgaacggaactaaccaactattgcagGTGGAATGTACCATACCAAAAGACGATGGAACTCTAGCATCCTTTGTTGGATTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03910.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g58040.3 (Oryza sativa), 3'ss of exon 2
----------------------------------------------------------------------------------------gttcgatgttttcctctgttttcttcttccatctataacagatctgcagaaccgatccggttcaagatcatttgaacggaactaaccaactattgcagGTGGAATGTACCATACCAAAAGACGATGGAACTCTAGCATCCTTTGTTGGATTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
||||| | || || | | || ||| | | || || | | | | | | | | ||| ||||| ||||| || || || ||||| ||||| ||| ||||||| | |||||| || || || |||||||||||||| || || || ||||| ||||||||||
gtgatgattctagggcagttttcttgagatctggtaacctgtgctctttggcttcacttgctcgaagtggtttcctgatgaacatgagagagaatgttgaaaaattcttgctgtgacggggttcaatggattaaagggctc--tctttttggtgttgagtgacaagaagtttgtggttgatttcagGTTGAATGCACAATTCCGAAAGATGATGGGACTTTAGCATCTTATGTTGGGTTTAGGGTCCAACACGACAATGCTAGGGGACCTATGAAGGGTGGAATCA
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 2
--------gttcgatgttttcctctgttttcttcttccatctataacagatctgcagaaccgatccggttcaagatcatttgaacggaactaaccaactattgcagGTGGAATGTACCATACCAAAAGACGATGGAACTCTAGCATCCTTTGTTGGATTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
| |||| ||| | | ||||| || | | || ||||| ||| || || | || || || | ||| || || | ||||||| || |||||||| || ||||| ||||||| | || | ||||||||||||||||||||||| || ||||| ||||| ||||||||||| || ||||
tgatggcaccttgatggcttctgttttgttcttattttgtatttatcagataagcataa--aatgcaactctagttc--taaaacatgttgaatgaa--aatgcagGTTGAGTGTACCATCCCCAAAGATGATGGAAGCTTGGCCACTTTTGTTGGATTCAGAGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGGATCA
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G28770.1 (Glycine max), 3'ss of exon 1
--------------gttcgatgttttcctctgttttcttcttccatctataacagatctg------cagaaccgatccg----gttcaagatcatttgaacggaactaa----ccaactattgcagGTGGAATGTACCATACCAAAAGACGATGGAACTCTAGCATCCTTTGTTGGATTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
| |||||| | | ||| |||| || || | || | | || | | | ||||| | | | | | || | | | || ||||||| |||||||||||||| ||||| ||||| || | ||| | |||||| ||||| |||||||| || ||||| ||||| ||||||||||| |||||||
gcaagtaaaattacttcttgtgtttttcatttctttgttctggcaaaattagtttacttgttttcactgtactgtttcatatagttcaccaactctagctctaaatcatgtttcacaataatgcagGTTGAATGTACCATACCTAAAGATGATGGCACGTTGCAATCTTATGTTGGGTTCAGGGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGAATCA
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 2
------------gttcgatgttttcctctgttttcttcttccatctataacag---atctgcagaaccgatccggttcaagatcatttg--aac---ggaactaaccaactatt----------gcagGTGGAATGTACCATACCAAAAGACGATGGAACTCTAGCATCCTTTGTTGGATTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
| | ||| | | | | ||| ||| | | | || | || | || | ||| | || || ||| | |||| || | || |||||| |||||||||||||| ||||| ||||| || | ||| | ||| || ||||| |||||||| || ||||| ||||| ||||||||||| |||||||
gcacgtaaaattgcttcttgtgtgttttcatgtccttgttctggcaaaattagtttacttgttttcactatactgtttcatatagttcaccaactctagttctaaataaatgtttcacaataatgcagGTTGAATGTACCATACCTAAAGATGATGGCACCTTGCAATCTTATGTAGGGTTCAGGGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGAATCA
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 1
gttcgatgttttcctctgttttct---tcttccatctataacagatctgcagaaccgatc--cggttcaagatcatttgaacggaactaaccaactattgcagGTGGAATGTACCATACCAAAAGACGATGGAACTCTAGCATCCTTTGTTGGATTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
|| ||||| | || | || |||| | |||| | || | | | | | || | | || | | | || |||||| ||||||||||| || ||||| ||||| | | || | |||||||||||||| ||||||| || ||||| ||||| ||||||||||| || ||||
--tcatagttttgttgtgcatactatgtctttaacatatatgatatgcataacatagtttagcaactcctccagttctaaatcttgttgaatgaaaat-gcagGTTGAATGTACCATCCCCAAAGATGATGGCAGCTTGGCCACTTTTGTTGGATTCAGGATTCAACATGATAATGCTAGAGGCCCCATGAAAGGAGGGATCA
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 3
-----gttcgatgttttcctctgttttcttcttccatctataacagatctgcagaaccgatccggttcaagatcatttgaacggaactaaccaactattgcagGTGGAATGTACCATACCAAAAGACGATGGAACTCTAGCATCCTTTGTTGGATTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
| ||| | | ||| ||||||| | ||||| ||||| | | | | | | | || ||| | | | ||| ||||||||| || || |||||||| ||||||||||| ||| | ||||| |||||||||||||| |||||||| |||||||| ||||| |||||||| || || ||||
gtggtttctaatgatatgctcagttttct-catccatg-ataaccgtatgatttaccattttttgactatgctcttttcacttcttttgaacaaa-attgcagGTTGAGTGCACCATACCCAAAGACGATGGTACTTTGGCATCATTTGTTGGATTCAGGGTTCAACATGACAATGCTAGAGGCCCCATGAAGGGAGGGATCA
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S62_236V6.7 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------gttcgatgttttcc--tctgtt-----ttcttcttccatctataacagatctgc---agaaccgatccggttc----aagatcatt--------------tgaacggaactaaccaactattgca--gGTGGAATGTACCATACCAAAAGACGATGGAACTCTAGCATCCTTTGTTGGATTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
|| ||||||||| ||| | | | | || ||| || ||| ||| |||| | || | | || || | | || || |||| | ||| || ||| |||||||| || || ||||||||||||||||| ||||||| | |||||| |||| || || ||||| | | || | ||||| || || ||
gtttggcttgcagcctgtgcggccatgccccaagacttaatacacttcagctaatatgcaattatatgttttccagcctgacaaccatcccacacaagttaattacaaatttgcttgagaggcgatgtgttttcttaagggtctttctcagtttggtttctaaccgtaatcgaccatccatttcatagGTTGAATGTACTATTCCCAAAGACGATGGAACTCTGGCATCCTACATCGGATTCCGAGTGCAGCATGACAACTCCCGTGGCCAAATGAAGGGCGGCATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcagaaccgatccggttcaagatcatttgaacggaactaaccaactattgcagGTGGAATGTACCATACCAAAAGACGATGGAACTCTAGCATCCTTTGTTGGATTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
aactaac putative branch site (score: 1)
atcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgatgttttcctctgttttcttcttccatctataacagatctgcagaaccgatccggttcaagatcatttgaacggaactaaccaactattgcagGTGGAATGTACCATACCAAAAGACGATGGAACTCTAGCATCCTTTGTTGGATTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA