Sequence
atgc intronic sequence ATGC exonic sequencegtttagcaggaaaatcctatcatctctctttagtagtgatatccttgttttggtataaattaaggcttacgattgttgttttttctttgtgataatttagAGTTATGCAAGATAGGAAACGAAGAGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G62700.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
-----------gtttagcaggaaaat-----cctatcatc--tctctttagtagtgatatccttgttttggtataaattaaggcttacgattgttgttttttctttgtgataat-ttagAGTTATGCAAGATAGGAAACGAAG-AGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA
|| || | | | || | ||| || | | | | || | | | || || | | ||| | | || | | | | | || ||| | | || || || |||||| ||||||||||||||| || || || ||||||||||| || ||||| || | |||||
gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA------------
upper sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------gtttag-caggaaaatcctatcatctctctttagtagtgatatccttgt---tttggtataaattaaggcttacgattgt------------------tgttttttctttgtgataatttagAGTTATGCAAGATAGGAAACGAAGAGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA
| | || | | | | | | | | | | | | | ||||| | ||| || ||| ||| || | | | | | | |||| | ||| |||| ||| |||| ||||||||||| ||| ||||||||||| || || || ||||||||||| || || || ||||| ||||| ||||| ||||
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
upper sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G315140_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------gtt--tagcaggaaaatcctatcatctctctttagtagtgatatccttgttttggtataaattaaggcttacgattgttgttttttctttgtgataatttagAGTTATGCAAGATAGGAAACGAAGAGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA
||| ||| || || | | ||| | | || || || | || | | | | | | | | | || || |||| |||||||| || | || ||||||| ||| ||||||||||| || || || ||||||||||| || ||||| ||||| ||||| | || || |
gcaagaaataaatacattccgaaagcaagtagttgatgcaatggagttggtagtagacaattacatgcatatatacac-gtgctgctaattaaatattag-actcacaatgatcaattggcatcacacatgcatttggaatgggcagAGAAGTGCAAGATTGGGATGGAGGAGCAGAACGATTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGCACTCGCACCAACCGGGCGACCAC
upper sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G03340.1 (Glycine max), 3'ss of exon 1
----gtttagcaggaaaatcctatcatctctctttagt--agt-----gatatccttgttttggtataaattaagg--cttacgattgttgttttttctttgtgataatttagAGTTATGCAAGATAGGAAACGAAGAGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA
|| | | || | | || | | | ||| || | | |||||| | | || | |||||| || | ||||| | |||| |||||||| ||||||| ||| || | | |||||||| |||||||||||||||||||||||||| ||||| || ||||| ||||||||||| || ||
gtacgtatgatatataagcctagctagcttcttatgattaagtctccaattagaaatacatatatataaaccacagtactgctcacatttgtttatttctgatgata-tatagAATTATGCAAAATAGGAAGCGATGAAGAAAATGAATGGTATTTCTTTAGTCATAAAGACAAGAAGTACCCCACTGGGACTCGTACCAATAGAGCTACAAA
upper sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G14700.1 (Glycine max), 3'ss of exon 1
-----gtttagcaggaaaatcctatcatctct--cttta---gtagtgatatccttgttttggtataaattaaggcttacgattgttgttttttctttgtgataatttagAGTTATGCAAGATAGGAAACGAAGAGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA
|| | || | || | | ||| | | | | ||| | || || || | | | ||| || | || || ||| |||||||| ||||||| ||| || || || || ||||| ||||||||||||||||| ||||| ||||| || |||||||| ||||||||||| || ||
gtaattcttcatacaaagctttcattaatcaaagcattacatacaattaagaacatgtatcatagtatatatagtatataaactcacatttgttactcatgtaaac--agAATTATGCAAAATAGGAACCGATGAACAAAGTGACTGGTATTTCTTTAGTCATAAAGATAAGAAATATCCAACTGGAACTCGCACCAATAGAGCTACAAA
upper sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G04250.1 (Glycine max), 3'ss of exon 1
gtttagcaggaaaatcctatcatctctctttagtagtgatatccttgttt--tggtataaattaaggcttacgattgttgttttttc----tttgt-gataattta----gAGTTATGCAAGATAGGAAACGAAGAGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA
|||| | | | ||| | | || || | || | || ||| | | || ||| | | | | ||||| | | || || || ||||||| ||||||| ||| || || || || ||||||||||| ||||||||||| ||||| ||||| || |||||||| ||||||||||| || ||
-----------aaatatttttttttcttaatggaagcattacatatagttaataacatgaatcatagtatataatttatatactgacataatttgttgctcatgtaaacagAACTATGCAAAATAGGAACCGATGAACAAAGTGACTGGTACTTCTTCAGTCATAAAGATAAGAAATATCCAACTGGAACTCGCACCAATAGAGCTACAAA
upper sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0154g00020.t01 (Vitis vinifera), 3'ss of exon 1
---------gtttagcaggaaaatcctatcatctctctttagtagtga-tatccttgttttggtataa-attaaggcttacgattgttgtttt------ttctttgtgataattt----agAGTTATGCAAGATAGGAAACGAAGAGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA
||| | | |||| | | | | | || | ||| | | ||| | || | || | | | | || || | ||| | |||||| |||||||||||| ||||| | |||||||||| || ||||| |||||||| |||||||| ||||||||||| || ||||||||||| |||||||| || ||
gtatgtagctcttattcctacagtccttccctatgcatacaacagaaaatatgtatatcttgatgaaatactatgcatcataaaatctgacttccatgttcatttttcttaatttgaatagAGTTATGCAAAATAGGCACTGAAGAGCAGAATGAGTGGTATTTCTTTAGCCATAAAGATAAGAAGTATCCAACTGGAACTCGAACTAATAGAGCTACAAA
upper sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
gtttagcaggaaaatcctatcatctctctttagtagtgatatccttgttttggtataaattaaggcttacgattgttgttttttctttgtgataatt-tagAGTTATGCAAGATAGGAAACGA---------AGAGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA
| | | | | | || || | || || | | || ||| | | ||| | | | | | ||| |||| |||||||||| | ||| | |||| | | |||||||||||||| ||||| ||||||||||| ||||| || | || |||| |
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaagg-aagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
upper sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 1
gtttagcaggaaaatcctatcatctctctttagtagtgatatccttgttttggtataaattaaggcttacgattgttgttttttctttgtgataattt---agAGTTATGCAAGATAGGAAACGAAGAGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA
|||| | | ||| | ||| | | | | || | ||| | || | | ||| |||| || ||||| ||| | || || | |||||||||||| || ||||| || |||||||||||||||||||||||||| ||||| ||||||||
-----------------------------gtagtctagtctcctccatttcgatatgattgcacaccactgacacctctttcattgttcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC
upper sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ18283 (Selaginella moellendorffii), 3'ss of exon 1
gtttagcaggaaaatcctatcatctctctttagtagtgatatccttgttttggtataaattaaggcttacgattgttgttttttctttgtgataattt---agAGTTATGCAAGATAGGAAACGAAGAGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA
|||| | | ||| | || | | | | || | ||| | || | | ||| |||| || ||||| ||| | || || | |||||||||||| || ||||| || |||||||||||||||||||||||||| ||||| ||||||||
-----------------------------gtagtctagtctcctccatttcgacatgattacacaccactgacacctctttcattgttcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttttggtataaattaaggcttacgattgttgttttttctttgtgataatttagAGTTATGCAAGATAGGAAACGAAGAGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA
ggcttac putative branch site (score: 3)
ttttttctttgtgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttagcaggaaaatcctatcatctctctttagtagtgatatccttgttttggtataaattaaggcttacgattgttgttttttctttgtgataatttagAGTTATGCAAGATAGGAAACGAAGAGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT