Sequence
atgc intronic sequence ATGC exonic sequence...ttctcatcttcgcaattcacgtgagctagttattaatttttctactgatgtatgattttatatgaaagactaaatttctctcgcggtgtcatggatatagACCATGAAGTCCTACATCTGGCTTCAAACTGCTGATGGTTCAATCCAGCAAGTGGAACAAGAGGTTGCAATGTTCTGTCCCATGATTTGTCAAGAGGTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G45950.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G45950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G109725_T04 (Zea mays), 3'ss of exon 3
ttctcatcttcgcaattcacgtgagctagttattaatttttctactgatgtatgattttatatgaaa-gactaaatttctctcgcggtgtcatggatatagACCATGAAGTCCTACATCTGGCTTCAAACTGCTGATGGTTCAATCCAGCAAGTGGAACAAGAGGTTGCAATGTTCTGTCCCATGATTTGTCAAGAGGTAA
| |||| | || | ||| | |||| | | | | | || || | || | | | | |||| | | | || | | ||| | || ||||||||||| ||||||||| || ||||||||||| | ||||||||||||||||| |||||||| |||| || |
-----------gtaattagagggaagcaattact----tttccaatcttatgcggttcaattcagcctgtcttgagcttattggtggtgaactata-acagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG
upper sequence: AT2G45950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G109725_T03 (Zea mays), 3'ss of exon 2
-------------ttctcatcttcgcaattcacgtgagctagttattaatttttctactgatgtatgattttatatgaaa-gactaaatttctctcgcggtgtcatggatatagACCATGAAGTCCTACATCTGGCTTCAAACTGCTGATGGTTCAATCCAGCAAGTGGAACAAGAGGTTGCAATGTTCTGTCCCATGATTTGTCAAGAGGTAA
| | || | | | ||| | | | | ||||| | | | | | || || | || | | | | |||| | | | || | | ||| | || ||||||||||| ||||||||| || ||||||||||| | ||||||||||||||||| |||||||| |||| || |
gtacaatcccctgcagcccccctctccggtaattagagggaagcaattacttttccaatcttatgcggttcaattcagcctgtcttgagcttattggtggtgaactata-acagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG
upper sequence: AT2G45950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G055785_T01 (Zea mays), 3'ss of exon 2
------ttctcatcttcgcaattcacgtgagctagttattaatttttctactgatgtatgattttatatgaaagactaaatttctctcgcggtgtcatggatatagACCATGAAGTCCTACATCTGGCTTCAAACTGCTGATGGTTCAATCCAGCAAGTGGAACAAGAGGTTGCAATGTTCTGTCCCATGATTTGTCAAGAGGTAA
|| |||||| | | | || ||| | | | | | | | || || | | | ||| | | | |||| | | |||| ||||| | || ||||||||||| ||||||||| || || |||||||| | ||||||||||||||||| |||||||| ||||| || |
gtaataaaaccagaggttcaattccctgcaccc--ttcttagctgcaactccgctctgttaattcatcctatg--ttgagtttat-tggtggtgaactata-atagGTGTTGAAGACATATATCTGGCTTCAGTGCTTTGATGGTTCCATACAACAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCAGGAAATTG
upper sequence: AT2G45950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G01090.2 (Glycine max), 3'ss of exon 1
---ttctcat-cttcgcaattcacgtgagctagttattaatttttctactgatgtatgattttatatgaaagactaaatttctctcgcggtgtcatggatatagACCATGAAGTCCTACATCTGGCTTCAAACTGCTGATGGTTCAATCCAGCAAGTGGAACAAGAGGTTGCAATGTTCTGTCCCATGATTTGTCAAGAGGTAA
| || | | || | | | || | ||| | || | || | ||| || || ||| | ||| ||| | | ||| |||||| || |||||||||| ||| | |||| ||||||||| |||||||||||||| |||||||||| || || |||| |||||||| |||
aaaaattaatgcaatgaaacttccctacaagagaatcaagaccttccattggt-tactttcttacattgaaactgaaactcttctttgtttgtatt---ttcagATGATGAAGCTGTATGTCTGGCTTCAGACTTCAGATGATTCAATCCAACAAGTGGAACAAGAAATTGCAATGTTTTGCCCACTGATATGTCAAGAAATAA
upper sequence: AT2G45950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G39480.1 (Glycine max), 3'ss of exon 2
ttctcatcttcgcaattcacgtgagctagttattaatt-tttctactgatgtatgattttatatgaaagactaaatttctctcgcggtgtcatggatatagACCATGAAGTCCTACATCTGGCTTCAAACTGCTGATGGTTCAATCCAGCAAGTGGAACAAGAGGTTGCAATGTTCTGTCCCATGATTTGTCAAGAGGTAA
| || | || || | | ||| || || | | || | | |||| | | | | | | | | | | | || ||| |||||| | || ||||||||| | || | |||||||||||||| |||||||||||||| ||||||||| || || ||||||||||||| |||
gtttctaaattataactcctggctttgtgatatcttttacttttgtttatttctcttttttcctaataaattctttattttatatatt-taaaaaattcagATGATGAAGCCTTATATCTGGCTTGAGACATCCGATGGTTCAATCCAACAAGTGGAACAAGAAATTGCAATGTATTGCCCTCTGATTTGTCAAGAAATAA
upper sequence: AT2G45950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G46780.1 (Glycine max), 3'ss of exon 1
ttctcatcttcgcaattcacgtgagc--tagttattaatttttctactgatgtatgattttatatgaaagactaaatttctctcgcggtgtcatggatatagACCATGAAGTCCTACATCTGGCTTCAAACTGCTGATGGTTCAATCCAGCAAGTGGAACAAGAGGTTGCAATGTTCTGTCCCATGATTTGTCAAGAGGTAA
|| | | ||| || | | || | | | || | | || | | | || | | | | | ||| | | || || ||| |||||| | || ||||||||| | || | |||||||||||||| |||||||||||||| ||||||||| || || ||||||||||||| |||
tttttgttttctatttttttttcctctgtaatatctcttacttttgtttatttctcttctttcctaataaattc--tttattttatatatacaaaaattcagATGATGAAGCCTTATATCTGGCTTGAGACATCAGATGGTTCAATCCAACAAGTGGAACAAGAAATTGCAATGTATTGCCCTCTGATTTGTCAAGAAATAA
upper sequence: AT2G45950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G07600.1 (Glycine max), 3'ss of exon 2
---ttctcatcttcgcaattcacgtgagctagttattaat-ttttctactgatgtatgattttatatgaaagactaaatttctctcgcggtgtcatggatatagACCATGAAGTCCTACATCTGGCTTCAAACTGCTGATGGTTCAATCCAGCAAGTGGAACAAGAGGTTGCAATGTTCTGTCCCATGATTTGTCAAGAGGTAA
| || | | || | | | || || || | || | || | ||| | || ||| | ||| ||| | | ||| |||||| | || | |||||||| ||| | |||| ||||||||| |||||||||||||| |||||||||| | || |||| |||||||| |||
aaaaattaatgctaggaaacttccctaccagagaatcaagaccttgcattggt-tactttcttacgttgaaactgaaactattctttgtttgtatt---ttcagATGATGAAGCCGTATGTATGGCTTCAGACTTCAGATGATTCAATCCAACAAGTGGAACAAGAAATTGCAATGTTTTCCCCACTGATATGTCAAGAAATAA
upper sequence: AT2G45950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv15s0046g02450.t01 (Vitis vinifera), 3'ss of exon 1
ttctcatcttcgcaattcacgtgagctagtta--ttaatttttctactgatgtatgattttatatgaaagactaaatttctctcgcggtgtcatggatat--agACCATGAAGTCCTACATCTGGCTTCAAACTGCTGATGGTTCAATCCAGCAAGTGGAACAAGAGGTTGCAATGTTCTGTCCCATGATTTGTCAAGAGGTAA
|| | || | | | | ||||||||| | | | || || | | | || | | | || || || || ||| |||||||||||||| ||||| || |||||||||||||||||||| |||| |||||||| || || ||||| || ||| |||| ||| | || |||
----ttggtttgatataaagataaatttccctatttaatttttgtggtcttttaagagtgattgatgattctgaagctacaatggcactgctatacattctcagATGATGAAGTCCTACATTTGGCTCCAGACTGCTGATGGTTCAATCCAAGAAGTAGAACAAGAAGTGGCCATGTTTTGCCCCTTGATATGTGATGAAATAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatgtatgattttatatgaaagactaaatttctctcgcggtgtcatggatatagACCATGAAGTCCTACATCTGGCTTCAAACTGCTGATGGTTCAATCCAGCAAGTGGAACAAGAGGTTGCAATGTTCTGTCCCATGATTTGTCAAGAGGTAA
gactaaa putative branch site (score: 2)
tatgattttatatgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctcatcttcgcaattcacgtgagctagttattaatttttctactgatgtatgattttatatgaaagactaaatttctctcgcggtgtcatggatatagACCATGAAGTCCTACATCTGGCTTCAAACTGCTGATGGTTCAATCCAGCAAGTGGAACAAGAGGTTGCAATGTTCTGTCCCATGATTTGTCAAGAGGTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - catcttc
- - - - - - caattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaagac