Sequence
atgc intronic sequence ATGC exonic sequencegtatactttttggtatcttatacctgcttatatttcatcatggtaaaacttcttacaagcttgtaattaaccaccacagGTTTTAAAAAGTCACTGTTCAATGTGTTTCTCGATGGAACCTGCCATCCAAAGATGGCATTGGTAATTGATGATCGATTGAAAGTTTGGGATGAGAAGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21670.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os04g44710.2 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------------------------------------------------------------gtatactttttggtatcttatacctgcttatatttcatcatggtaaaacttcttac------aagcttgtaattaaccacc---acagGTTTTAAAAAGTCACTGTTCAATGTGTTTCTCGATGGAACCTGCCATCCAAAGATGGCATTGGTAATTGATGATCGATTGAAAGTTTGGGATGAGAAGGA
| | ||| | | || | ||| | | | || | | || || | | | | | | ||||| | ||| | | |||||| ||| | ||||| || | ||||| | ||||| ||| | ||||| | || ||||||||||| |||||||||||||||||||| ||
gtaggtgttagcattactattactttcaaacaacacaactaccaaaggaatatagtgtcatttggtatattttgtacaccgcaatcaatgttttgtgttgtctaatttccttcatacaaatttccatgtgcatgaacataat-gtcttggaattttccatcttttgacgttaatgctacaccactcttatagGCTCTCGAAAGTCTCTGCTGAATGTATTCCATGATGGGTCTTGCCACCCAGAAATGGCCCTAGTGATTGATGATCGCTTGAAAGTTTGGGATGAGAAAGA
upper sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------------------------------gtatactttttggtatcttatacctgcttata-tttcatcatggtaaaacttcttacaagcttgtaattaaccaccacagGTTTTAAAAAGTCACTGTTCAATGTGTTTCTCGATGGAACCTGCCATCCAAAGATGGCATTGGTAATTGATGATCGATTGAAAGTTTGGGATGAGAAGGA
| ||| | || || | || || |||||| | | ||| | | ||| || ||| | |||||| |||||||| || | ||||| || | ||||| | |||||||| |||||||| |||||||||||||| ||||||||||||||||||||||
gtatgtaattcatcttgtttttgaacaagtacaaaaagagcattagcctaatgtggcctaaatgttgtcatactcaaaagttgacaaactgtgaaaaatacaattcaaatttttagtttcattctactgaaattaatgccaaatttcctatt------tatagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA
upper sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G31430.1 (Glycine max), 3'ss of exon 3
-----------gtatactttttggtat-cttatac-----ctgcttatatttcatca--tggtaaaacttct--tacaagcttgtaattaaccaccacagGTTTTAAAAAGTCACTGTTCAATGTGTTTCTCGATGGAACCTGCCATCCAAAGATGGCATTGGTAATTGATGATCGATTGAAAGTTTGGGATGAGAAGGA
| ||| | ||| | | | | ||| || | ||| || | || | |||| | || || ||| | || |||||||| || |||||| |||||||||| || | ||||| ||||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||
atgctttattattgtaccatacaatatgcctgtgcttttgctggttctgtttaatttacttgtcatacttataatatggtatttcaataatacaatacagGTTTGAAGAAGTCATTGTTCAATGTCTTCCAAGATGGTTTATGCCATCCAAAGATGGCATTGGTAATTGATGATCGCTTGAAAGTGTGGGATGAGAAGGA
upper sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G25010.1 (Glycine max), 3'ss of exon 3
-------------gtatactttttgg-tatcttatacctgcttatatttcatca--tggtaaaacttcttacaagcttgt-----aattaaccaccacagGTTTTAAAAAGTCACTGTTCAATGTGTTTCTCGATGGAACCTGCCATCCAAAGATGGCATTGGTAATTGATGATCGATTGAAAGTTTGGGATGAGAAGGA
|||| | || | | || | ||||| | ||| | | || | |||| | | | | | || ||| | | |||||||| || |||||| |||||||||| || | ||||| | || ||||||||||||||||||||||||||||||| |||||||| |||||||||| |||
ctttatttttgtaccataccatatgcctgtgtttttgctgctgctgtttagtttgcttgtcatacttataatatgatggtgtttcaataatataatacagGTTTGAAGAAGTCATTGTTCAATGTCTTCCAAGATGGTTCATGTGATCCAAAGATGGCATTGGTAATTGATGATCGCTTGAAAGTGTGGGATGAGAGGGA
upper sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G31510.1 (Glycine max), 3'ss of exon 3
---------------------gtatactttttggtatcttatacctgcttatatttcatcatggtaaa-acttcttacaagcttgtaattaaccaccacagGTTTTAAAAAGTCACTGTTCAATGTGTTTCTCGATGGAACCTGCCATCCAAAGATGGCATTGGTAATTGATGATCGATTGAAAGTTTGGGATGAGAAGGA
| | | | | | || |||| | || | || | |||||| | || ||| | | | |||||| || || ||| |||| ||||| || | |||| ||||||| |||||||||||||||||||||||||| |||||||| ||||||||||| ||
aatagctcgaattttaaattttcaaattcatagcagtttttctgctgcaactgttcatttattttttgtgcttcttgtgtgttt-caatatattataatagGTTTAAAGAAATCATTGTTTAATGTATTCCAAAATGGCTTATGCCATCTGAAGATGGCATTGGTAATTGATGATCGCTTGAAAGTGTGGGATGAGAAAGA
upper sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G07800.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------------------------------------------------------gtatactt--tttggtatcttatacctgcttatatttcatcatggtaaa---acttcttacaagcttgtaattaaccac--cacagGTTTTAAAAAGTCACTGTTCAATGTGTTTCTCGATGGAACCTGCCATCCAAAGATGGCATTGGTAATTGATGATCGATTGAAAGTTTGGGATGAGAAGGA
|||| | ||| | | ||||| | || | | | || | | || || ||| || | | | |||||| || || || |||| ||||| || | |||| ||||||| |||||||||||||||||||||||||| ||||||| ||||||||||| ||
gtaagtggcatttttttaaaattctattatccttgttttcaaatgagaagctttacatgtgtaattgagtagataaagggagcaaataaaaaggatgacaatagcttgtattttaaattttaaaattcataccagtttttctgctgcaactgttcatttattttttgtgtttatgtgtttcaatatataatagGTTTAAAGAAATCGTTGTTTAATGTATTCCAAAATGGCTTATGCCATCTGAAGATGGCATTGGTAATTGATGATCGCCTGAAAGTGTGGGATGAGAAAGA
upper sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0370g00040.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------------------------------------------------------------gta--tactttttggtatcttatacctgcttatatttcatcatggtaaaacttcttacaagcttgtaattaaccaccacagGTTTTAAAAAGTCACTGTTCAATGTGTTTCTCGATGGAACCTGCCATCCAAAGATGGCATTGGTAATTGATGATCGATTGAAAGTTTGGGATGAGAAGGA
||| | | ||| ||| | || | || | ||| | | || |||| | | ||||| | ||| | | |||||||||||||||||| |||| ||||||| ||||||||| |||||||| || |||||||||||||| |||||||| |||||||| || ||
gtaagtttttaaaagaaatggttgatcttagggatgacttatgccatccacagcagaccaaagacaagctaattaattatatagcttctgatatgattttttttcacccattcttgtagttgttacttgttattctgtaaac-cacgtacattatcctcaatatcctacttatt--ttctttattaaatttgatagGCTCAAGAAAGTCACTGTTCAATGTCTTTCAAGATGGAATCTGCCATCCTAAGATGGCTTTAGTAATTGATGATCGTTTGAAAGTGTGGGATGAAAAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttatatttcatcatggtaaaacttcttacaagcttgtaattaaccaccacagGTTTTAAAAAGTCACTGTTCAATGTGTTTCTCGATGGAACCTGCCATCCAAAGATGGCATTGGTAATTGATGATCGATTGAAAGTTTGGGATGAGAAGGA
aattaac putative branch site (score: 2)
ttgtaattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatactttttggtatcttatacctgcttatatttcatcatggtaaaacttcttacaagcttgtaattaaccaccacagGTTTTAAAAAGTCACTGTTCAATGTGTTTCTCGATGGAACCTGCCATCCAAAGATGGCATTGGTAATTGATGATCGATTGAAAGTTTGGGATGAGAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG