Sequence
atgc intronic sequence ATGC exonic sequencegtattagttaattggagcttctaatacttgatctcaggtatcaaatgctaatcttggctttgtggtatttcatgcagACTCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G21520.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G21520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 6
------gtattagttaattggagcttctaatacttgatctcaggtatcaaatgctaatcttggctttgtggtatttcatgcagACTCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTC
| | | || || || | ||| | | | | ||| | ||||| | || || |||||||| |||||||||||||| ||||||| || || || || ||||||| ||||||||||| ||| ||||||||| || || || | || || || |
gtatgagcctcattttttttacactctcttttgttgtttttttgcttggaatatattgggttaatttgttgcatctc---cagACTCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATAC
upper sequence: AT2G21520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G01220.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------gtattagttaattggagcttctaatacttgatctcaggtatcaaatgctaatct-tggctttgtggtatttcatgcagACTCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTC
| | ||||| ||| | ||| || | |||| | | || | | || | | | | | || |||||||| ||||||||||||||| ||||| ||||||||||||||||| | ||||||||||||||| ||||| || || || ||| || |||| ||||
gtgtgttgtcttgttccctgtcacgtgtaattaattgctattttcttttggaatgctggttttgtcagtta-ttgcaaattcgaa-agatgatatactatggtaacagtggactgatgattcttttattaatgatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAACACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
upper sequence: AT2G21520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G01260.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------gtattagttaattggagcttctaatacttgatctcaggta-tcaaatgctaatcttggctttgtggtatttcatgcagACTCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTC
| | ||||| ||| | ||| ||| | ||| || || ||| | | || | | | | | || |||||||| ||||||||||||||| ||||| ||||||||||||||||| | |||| |||||||||| ||||| || || || ||| || |||| ||||
gtgtgttgtcttgttccctgtgtaattgtttgctattttcttttggaatgctagttttgtcagtta-ttgcaaattcaaatgat-gatatcctatagtcagaatggaccaatgattcttttattaataatacagACTCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAGCACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTC
upper sequence: AT2G21520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G04460.1 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------gtattagttaattggagcttct------aatacttgatctcaggtatcaa---atgctaatcttggctttgtggtatttc---------atgcagACTCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTC
|| || |||| | || | | | || || |||| |||| |||| || || ||| | | | | || ||||||||| |||||||||||| || ||||| || |||||||||||| | || ||||||||||||||| || ||||| || |||||| || | || ||||
gtgtgtaacactgtcggtttctgtgtattttgttacattacgccccttgttttgatttcatcggttatatgaaattaaaagtttttaaagaagaatatgtactaaggtctcaactattgctgattttttattttttatttctttttttaatgatacagACTCTCTGCCAAATGTTTATCATAAATGCTGGCCCTGGATTTAGGTTGCTATGGAACACTGTCAAGTCTTTCCTTGATCCCAAGACAACTTCAAAGATTC
upper sequence: AT2G21520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G12260.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------gtattagttaattggagcttctaata----cttgatctcaggtatcaaatg---ctaatcttggctttgtggtatttc---------atgcagACTCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTC
| ||| |||| | | || | | || || |||| |||| | || || | | ||||| | | || || ||||||||| |||||||||||| || ||||| || || ||||||||| | || ||||||||||||||| || ||||| || || ||| || | || ||||
gtgagtaacactgccggtttctgtgtattatggcccttattttgatttcatccgatataggaaattaaaattgtaaagaagaacatgtactaaggtctcaactttttctgattattgatttgttatttctcttcttaatgatacagACTCTCTGCCAAATGTTTATCATAAATGCTGGACCGGGATTTAGGTTGCTATGGAACACTGTCAAGTCTTTCCTTGATCCCAAAACAACTTCAAAGATTC
upper sequence: AT2G21520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------gtattagttaattggagct--tctaatacttgatctcaggtatcaaatgctaatcttggct-ttgtggtatttca-----tgcagACTCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTC
|| || ||| | | | | | ||||| | | | ||| | ||| | ||| | | | | ||||||||||| ||||||||||||||||||||| || ||||| |||||||| |||||||||||||| |||| ||||| || || || ||| || | || ||||
gtattcaacctttttctgttgacatgataagctatagttgtaatccatttcaaaattgatataggtgactgaatatgtgccctggatcttgaactctcttaactgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTCTGGAACACTGTAAAGACTTTTCTAGATCCCAAAACAACTTCCAAGATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatacttgatctcaggtatcaaatgctaatcttggctttgtggtatttcatgcagACTCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTC
tgctaat putative branch site (score: 2)
tatcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattagttaattggagcttctaatacttgatctcaggtatcaaatgctaatcttggctttgtggtatttcatgcagACTCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT