Sequence
atgc intronic sequence ATGC exonic sequencegtttgcccaatcccaccatctctatccttcattactttgtctctatttcctaaggaaagattttaaaagtctttttttattcgtttgtggaaatagAGTTGTGCAAAATTGGGCATGAAGAGCAGAGTGATTGGTACTTCTTTAGCCATAAAGACAAGAAGTATCCCACAGGGACTCGAACCAATAGAGCAACAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G12260.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G12260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------------------------------------------------gtttgcccaatcccaccatctctatccttcattactttgtctctatttcctaaggaaagattttaaaagtctttttt---tattcgtt-tgtggaaatagAGTTGTGCAAAATTGGGCATGAAGAGCAGAGTGATTGGTACTTCTTTAGCCATAAAGACAAGAAGTATCCCACAGGGACTCGAACCAATAGAGCAACAAA
| || | || | || | | | | || | | || | | | || || || | ||| | | || |||| ||| ||||| ||||| |||||||||| || ||||||||||| ||||| || ||||||||||| || || || ||||| ||||| ||||| || |
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGGATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC
upper sequence: AT1G12260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G315140_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------gtttgcccaatcccaccatctctatcctt---cattactttgtctctatttcctaaggaaagattttaaaagtctttttttattcgtttgtgg-aaatagAGTTGTGCAAAATTGGGCATGAAGAGCAGAGTGATTGGTACTTCTTTAGCCATAAAGACAAGAAGTATCCCACAGGGACTCGAACCAATAGAGCAACAAA
||| | | | | | | || | | | | | || | | | | | || | | | || | |||| |||| |||||| |||||| || ||||||| |||||||||||||| ||||| || ||||||||||| || || || ||||| ||||| | || || |
gcaagaaataaatacattccgaaagcaagtagttgatgcaatggagttggtagtagacaattacatgcatatatacacgtgctgctaattaaatattagactcacaatgatcaattggcatcacacatgcatttggaatgggcagAGAAGTGCAAGATTGGGATGGAGGAGCAGAACGATTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGCACTCGCACCAACCGGGCGACCAC
upper sequence: AT1G12260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G03340.1 (Glycine max), 3'ss of exon 1
----gtttgcccaatcccaccatctctatccttcattactttgtctctatttcctaaggaaagattttaaa----agt-ctttttttattcgtttgt--------ggaaatagAGTTGTGCAAAATTGGGCATGAAGAGCAGAGTGATTGGTACTTCTTTAGCCATAAAGACAAGAAGTATCCCACAGGGACTCGAACCAATAGAGCAACAAA
|| || || | | || | ||| || | | ||||| | || || | | |||| ||| || | ||| |||| | | ||||| || |||||||| || || || | | ||| ||||| |||||||| ||||||||||||||||| ||||| |||||||| ||||||||||| |||||
gtacgtatgatatataagcctagctagcttctt-atgattaagtctccaattagaaatacatatatataaaccacagtactgctcacatttgtttatttctgatgatatatagAATTATGCAAAATAGGAAGCGATGAAGAAAATGAATGGTATTTCTTTAGTCATAAAGACAAGAAGTACCCCACTGGGACTCGTACCAATAGAGCTACAAA
upper sequence: AT1G12260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G04250.1 (Glycine max), 3'ss of exon 1
---------gtttgcccaatcccaccatctc-tatccttcattactttgtctctatttcctaaggaaagattttaaaagtctttttttattcgtttgtggaaatagAGTTGTGCAAAATTGGGCATGAAGAGCAGAGTGATTGGTACTTCTTTAGCCATAAAGACAAGAAGTATCCCACAGGGACTCGAACCAATAGAGCAACAAA
||| | ||| | ||| | ||| || || || | || | ||| | || | | | ||| || | | || ||| ||| | |||||||| || || || || ||||| ||||||||||| || |||||||| ||||| ||||| || || ||||| ||||||||||| |||||
aaatatttttttttcttaatggaagcattacatatagttaataacatgaatcatagtatataatttat-atactgacataatttgtt-----gctcatgtaaacagAACTATGCAAAATAGGAACCGATGAACAAAGTGACTGGTACTTCTTCAGTCATAAAGATAAGAAATATCCAACTGGAACTCGCACCAATAGAGCTACAAA
upper sequence: AT1G12260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G14700.1 (Glycine max), 3'ss of exon 1
------gtttgcccaatcccaccatctct------atccttcattactttgtctctatttcctaa-ggaaagattttaaaagtctttttttattcgtttgtggaaatagAGTTGTGCAAAATTGGGCATGAAGAGCAGAGTGATTGGTACTTCTTTAGCCATAAAGACAAGAAGTATCCCACAGGGACTCGAACCAATAGAGCAACAAA
|| ||| | ||| | || | | | | | | || || | | | | || || ||| || | || ||| ||| || |||||||| || || || || ||||| ||||| |||||||| |||||||| ||||| ||||| || || ||||| ||||||||||| |||||
gtaattcttcatacaaagctttcattaatcaaagcattacatacaattaagaacatgtatcatagtatatatagtatataaactcacatttgtt-actcatgtaaacagAATTATGCAAAATAGGAACCGATGAACAAAGTGACTGGTATTTCTTTAGTCATAAAGATAAGAAATATCCAACTGGAACTCGCACCAATAGAGCTACAAA
upper sequence: AT1G12260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0154g00020.t01 (Vitis vinifera), 3'ss of exon 1
---------gtttgcccaatcccaccatctctatcctt-cattactttgtctctatttcctaaggaaagatttta------aaagtct---ttttttattcgttt------gtggaaatagAGTTGTGCAAAATTGGGCATGAAGAGCAGAGTGATTGGTACTTCTTTAGCCATAAAGACAAGAAGTATCCCACAGGGACTCGAACCAATAGAGCAACAAA
|| | | || || |||| | | || | | | ||| || | | |||| | | | ||| ||| || | ||| ||| | ||||||||| |||||||| || ||||||||||| ||| ||||| ||||||||||||||||| ||||||||||| || || |||||||| |||||||| |||||
gtatgtagctcttattcctacagtccttccctatgcatacaacagaaaatatgtatatcttgatgaaatactatgcatcataaaatctgacttccatgttcatttttcttaatttgaatagAGTTATGCAAAATAGGCACTGAAGAGCAGAATGAGTGGTATTTCTTTAGCCATAAAGATAAGAAGTATCCAACTGGAACTCGAACTAATAGAGCTACAAA
upper sequence: AT1G12260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------------------------------------------------gtttgcccaatccca--ccatctctatccttcattactttgtctctatttcctaag-----gaaagattttaaaagtcttttttta--ttcgtttgtggaaatagAGTTGTGCAAAATTGGGCATGA------AGAGCA---GAGTGATTGGTACTTCTTTAGCCATAAAGACAAGAAGTATCCCACAGGGACTCGAACCAATAGAGCAACAAA
| ||| | | | | | | || || || | | | |||| | | ||| || | | ||| | ||| |||||| || ||| | || |||||| ||||| ||||||||||| ||||| || || ||||||||||||||||| | || |||| |
gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaacagtactatccattgaattgtgatcaacataagctcaagagcatgttctcctcatctattgatagcatgaaatggtccagcagtattgacaaaaacttgttgcaccgatcagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG---------
upper sequence: AT1G12260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
----gtttgcccaatcccaccatctctatccttcattactttgt-ctctatttcctaaggaaagattttaaaagtctttttttattcgtttgtggaaatagAGTTGTGCAAAATT------GGGCAT---GAAGAGCAGAGTGATTGGTACTTCTTTAGCCATAAAGACAAGAAGTATCCCACAGGGACTCGAACCAATAGAGCAACAAA
| | | | | | | | || ||| | | | | |||||| | || | | | | | | |||| | ||||| ||| | ||| | | |||| | |||||||||||||||||||| ||||||||||| ||||| || | || |||| |
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattg-cagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG--------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctatttcctaaggaaagattttaaaagtctttttttattcgtttgtggaaatagAGTTGTGCAAAATTGGGCATGAAGAGCAGAGTGATTGGTACTTCTTTAGCCATAAAGACAAGAAGTATCCCACAGGGACTCGAACCAATAGAGCAACAAA
aaagattttaaaagtc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgcccaatcccaccatctctatccttcattactttgtctctatttcctaaggaaagattttaaaagtctttttttattcgtttgtggaaatagAGTTGTGCAAAATTGGGCATGAAGAGCAGAGTGATTGGTACTTCTTTAGCCATAAAGACAAGAAGTATCCCACAGGGACTCGAACCAATAGAGCAACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA