Sequence
atgc intronic sequence ATGC exonic sequence...tatatatatatatatatatatatatatagatatatatgcatgaaaagttcattgttatacaattctctaatttgtatgttatctttttattttttggaagAGAGATGCAAGATAGGATCAACACCACAAAACGAATGGTACTTCTTCAGCCACAAGGACAGGAAATATCCGACGGGGTCAAGGACCAACCGTGCTACTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G10350.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: 13113.m00212 (Oryza sativa), 3'ss of exon 1
---tatatatatatatatatatatatatatagatatatatgcatgaaaagttcattgttatacaattctctaatttgtatgttatct-ttttattttttggaagAGAGATGCAAGATAGGATCAACACCACAAAACGAATGGTACTTCTTCAGCCACAAGGACAGGAAATATCCGACGGGGTCAAGGACCAACCGTGCTACTCA
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ggtcggagatgtaaatcattttcattatctaagc-tctctccatcatgcatgcatggccatggaggtgacgggggt---tgccatttgttgcgtgtgtgtgcagAGAGGTGCAGGATCGGGTCGGCGCCGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACCGCAAGTACCCGACGGGGTCGAGGACGAACCGCGCCACGAC
upper sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G099144_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------------tatatatatatatatatatatatatatagatatatatgcatgaaaa-gttcattgttatacaattctctaatttgtatgttatc-----------tttttattttttgga--agAGAGATGCAAGATAGGATCAACACCACAAAACGAATGGTACTTCTTCAGCCACAAGGACAGGAAATATCCGACGGGGTCAAGGACCAACCGTGCTACTCA
|| || | | | | | || | | | | || || || || | ||| | |||| || ||| || || | || |||||| ||| ||| || || | || || ||||| |||||||||||||||||||||||| | || || ||||||||||| ||||| ||||| || ||
gtatagtgcttgggcatgttacgttcatggcttcatccttcatgcatggcgattcagttacatgcacgcagcttgttgtttagttgtttgtcttagcttgttcctgtggcttcctgcacagcacggtaatactcattacatcatgctcatccacttgcatcgatcggtgcagAGAGGTGCCGGATCGGGTCGGCGCCGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACCGCAAGTACCCGACGGGGTCCAGGACGAACCGCGCCACCAC
upper sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G435824_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------------tatatatatatatatatatat-atatatagatatatatgcatgaaaagttcattgtt-----atacaattctctaatttgtatgttatctttttattttttggaagAGAGATGCAAGATAGGATCAACACCACAAAACGAATGGTACTTCTTCAGCCACAAGGACAGGAAATATCCGACGGGGTCAAGGACCAACCGTGCTACTCA
|| || | | || | || | | | ||| |||| | | | | | || | || || | | || | | | ||||| ||| ||| || || | || || ||||| |||||||||||||||||||||||| | || || ||||||||||| ||||| ||||| || ||
gtatatatattatatacttggcaaataaaaaccagttcatgcccccatgcatgcatgcatgtccatggcgatcaatcaatcagttactacatgcaggcgcagccatgccggctgcagcttcttcttgttgagtcgttcgtcgctcatccacgtgaatccatcgttgcattgcatgcatcggatatatatgcagAGACGTGCCGGATCGGGTCGGCGCCGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACCGCAAGTACCCGACGGGGTCGAGGACGAACCGCGCCACGAC
upper sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 1
---tatatatatatatatata-tatatatatagatatatatgcatgaaaagttcattgttatacaattctctaatttgtatgttatctttttattttttggaagAGAGATGCAAGATAGGATCAACACCACAAAACGAATGGTACTTCTTCAGCCACAAGGACAGGAAATATCCGACGGGGTCAAGGACCAACCGTGCTACTCA
| | | |||| || ||| ||| | | |||| | | | | ||| || | || | ||| || || | | | | ||| | | | ||||||||| | ||| || || ||||||||||| || ||||||||||||||||||||||| ||||| ||||| || ||||||||||| || | || || |
caacagccaaacatatccctaatatttat-tggctatacttttgttgatgaattattattttg--atgttgtaacttagttgat-tttgtgtatatgtatgcagAGAGATGTAGGATTGGGTCCACACCACAAAATGAGTGGTACTTCTTCAGCCACAAGGATAGGAAGTATCCAACAGGGTCAAGGACTAATAGAGCCACAAA
upper sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------------------------------------tatatatatatatatatatatatatatagatatatatgcatgaaaagttcattgttatacaat-tctctaatttgtatgttatctttttatttt-------ttggaagAGAGATGCAAGAT-AGGATCAAC--ACCA------CAAAACGAATGGTACTTCTTCAGCCACAAGGACAGGAAATATCCGACGGGGTCAAGGACCAACCGTGCTACTCA
|| | | ||| | || | | | | | | | | | ||| | | || | | ||| | | | | ||| |||| ||| || | || |||| |||||||| |||||||||||||||||||| |||| || || || |||| | | |||||
gtaagaatcgatcagaatcctcggtgtactatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatggtgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccgatgtggtcatcagAAGTGTGCAGGATTGGGGACGACCCACCAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG---------
upper sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S102_187V6.1 (Physcomitrella patens), 3'ss of exon 1
---------tatatatatatat-atatatatatatatagatatatatgcatgaaaagttcattgttatacaattctctaatttgta-----tgttatctttttattttt-------tggaagAGAGATGCAAGATAGGA----TCAACACCA-----CAAAACGAATGGTACTTCTTCAGCCACAAGGACAGGAAATATCCGACGGGGTCAAGGACCAACCGTGCTACTCA-
| || | | | |||| | | | || | || | |||| ||||| | ||| || | | || | || |||||| || || | ||||| ||| || ||| |||| || | || ||||||||||||||||||||||| | ||||||||| ||| | | || || || ||
gcatgaacatgctcatttgaaggacatatttgagtttcgaatttctcccacatagagttt-ttgttttgggattggtggatatcttgatactgatgatattcaatttttgtggcgatgtcaggggtatgcagGATCGGGGACGTCACCACCGAAGACCAGAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAATATCCTTGCGGGAACCGTGCAAATCGAGCCACCGCC
upper sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------------------------------------tatatatatatatatatatatatatatagatatatatgcatgaaaagttcattgttatacaattctctaatttgtatgttatctttttattttttggaagAGAGAT--GCAAGATAGGATCAACACCACAAAACGAATGGTACTTCTTCAGCCACAAGGACAGGAAATATCCGACGGGGTCAAGGACCAACCGTGCTACTCA
|||||| ||| |||| ||||||||||| |||||||| |||| || | || || || |||| || || | | || || | | | | || | ||| ||||||||||||||||||||||||| ||||||||| || || | | |||||
gtaagccaacgaacccacattttgcaggatttcattaacgttggttgaggttagaaaactggaactcgctttagttcgaggaatatataaatagatatggatatatatatatatatatatatatgagaatactctaagtac-tgataacaccatctgtac-ttgcggcgacatcagAGGTGTGCAGAATTGGCGACGACGCACCCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG---------
upper sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
------------tatatatatatatatatatatatatatagatatatatgcatgaaaagttcattgttatacaattctctaatttgtatgttatctttttattt--tttg------gaagAGAGATGCAAGATAGGATCAACACCACAAAACGAATGGTACTTCTTCAGCCACAAGGACAGGAAATATCCGACGGGGTCAAGGACCAACCGTGCTACTCA
| | | | || | | | | | | | || || | ||| || | ||||| | | || ||| | ||| |||| ||| | ||| || || || | || |||| |||||||||||||||||||| |||| |||||| ||||| ||| | ||||||||| | || ||
gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 1
tatatatatatatatatatatatatatagatatatatgcatgaaaagttcattgttatacaattctctaatttgtatgttatc-tttttattttttggaagAGAGATGCAAGATAGGATCAACACCACAAAACGAATGGTACTTCTTCAGCCACAAGGACAGGAAATATCCGACGGGGTCAAGGACCAACCGTGCTACTCA
||| | | | | || || ||| | || | | | | || || || |||||| ||||| || ||||| |||||| | ||||| |||||||||||| ||||| |||||||||| ||| ||||| ||||| | | |||||| | || ||
-------------------------gtagtctagtctcctccatttcgatatgattgcaca--ccactgacacctctttcattgttcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC
upper sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
------------tatatatatatatatatatatatatatagatatatatgcatgaaaagttcat-tgttatacaattctctaatttgtatgttatctttttattt--tttg------gaagAGAGATGCAAGATAGGATCAACACCACAAAACGAATGGTACTTCTTCAGCCACAAGGACAGGAAATATCCGACGGGGTCAAGGACCAACCGTGCTACTCA
| | | | || | | | | | | | | | |||| | ||| || | ||||| | | || ||| | ||| |||| ||| | ||| || || || | || |||| |||||||||||||||||||| |||| |||||| ||||| ||| | ||||||||| | || ||
gtaagacggtcatccctcaagcttctcatttcgggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ18283 (Selaginella moellendorffii), 3'ss of exon 1
tatatatatatatatatatatatatatagatatatatgcatgaaaagttcattgttatacaattctctaatttgtatgttatc-tttttattttttggaagAGAGATGCAAGATAGGATCAACACCACAAAACGAATGGTACTTCTTCAGCCACAAGGACAGGAAATATCCGACGGGGTCAAGGACCAACCGTGCTACTCA
||| | | | | ||| ||| ||| | || | | | | || || || |||||| ||||| || ||||| |||||| | ||||| |||||||||||| ||||| |||||||||| ||| ||||| ||||| | | |||||| | || ||
-------------------------gtagtctagtctcctccatttcgacatgattacaca--ccactgacacctctttcattgttcttcgattttggcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttcattgttatacaattctctaatttgtatgttatctttttattttttggaagAGAGATGCAAGATAGGATCAACACCACAAAACGAATGGTACTTCTTCAGCCACAAGGACAGGAAATATCCGACGGGGTCAAGGACCAACCGTGCTACTCA
ctctaat putative branch site (score: 3)
ttatctttttattttt putative PPT
aattctctaatttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatatatatatatatatatatatatatagatatatatgcatgaaaagttcattgttatacaattctctaatttgtatgttatctttttattttttggaagAGAGATGCAAGATAGGATCAACACCACAAAACGAATGGTACTTCTTCAGCCACAAGGACAGGAAATATCCGACGGGGTCAAGGACCAACCGTGCTACTCA
- - - - - - - - - - - - - - - - - - - catgaaa