Sequence
atgc intronic sequence ATGC exonic sequencegttggaattattgtccttaccagccacatcctttgtagatctgaaggctgaccacattgcatacttgctttgcagATGGGGAAATATTTCACAGCATACAGGATTGATCATATATTGGGATTCTTCAGAATCTGGGAGCTTCCAGCTCATGCTATGACTGGTTTAGTGGGGAAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G40840.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G40840.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os07g46790.1 (Oryza sativa), 3'ss of exon 13
--------gttggaattattgtc-cttaccagccacatcctttgtagatctgaaggctgaccacattgcatacttgctttgcagATGGGGAAATATTTCACAGCATACAGGATTGATCATATATTGGGATTCTTCAGAATCTGGGAGCTTCCAGCTCATGCTATGACTGGTTTAGTGGGGAAGT
| | || |||| | | | | | | || | | | | | | | | | | |||| | ||||||| ||||| ||||| ||||| ||||| || ||||| ||||| ||||| || || ||||||||||||| |||||| || ||| |||| ||||| |
gttatttaatagcaaatattttttcctgtctggctggtcatcttttatcgtcattatttatcgccagttac-cttgttc--cagATGGCAAAATACTTCACTGCATATAGGATAGACCATATCTTGGGTTTCTTTAGGATATGGGAGCTTCCAGATCATGCAGCCACAGGTCTAGTTGGGAAAT
upper sequence: AT2G40840.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G136803_T02 (Zea mays), 3'ss of exon 3
gttggaattattgtccttaccagccacatcctttgtagatc----tgaaggctgacca--cattgcatacttgct--ttgcagATGGGGAAATATTTCACAGCATACAGGATTGATCATATATTGGGATTCTTCAGAATCTGGGAGCTTCCAGCTCATGCTATGACTGGTTTAGTGGGGAAGT
||||| | || ||| | || | | || | | | | ||| | |||| || |||||||||| || || ||||||||||||||||| || || || ||||| ||||| || || ||||||||||||| ||||||| || |||||||| ||||| |
------gttatttaacataacagtcgtatttctgactggtcatcttttccttttattattcatatcctactagcatgttgcagATGGCAAAGTACTTCACAGCATACAGGATAGACCACATCTTGGGTTTCTTTAGGATATGGGAGCTTCCAGATCATGCTGCAACAGGTTTAGTTGGGAAAT
upper sequence: AT2G40840.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA03G27600.1 (Glycine max), 3'ss of exon 13
-------------gttggaattattgtccttac-----cagcca--catcctttgt-agatctgaaggctgaccacattgcatacttgcttt---------------gcagATGGGGAAATATTTCACAGCATACAGGATTGATCATATATTGGGATTCTTCAGAATCTGGGAGCTTCCAGCTCATGCTATGACTGGTTTAGTGGGGAAGT
|| | ||||||||| || | ||||| || | || | ||||||| | || | ||| || ||||||| |||||||| ||||| |||||||||||||| ||||||||||||||| |||| ||||| ||||| | ||||||| ||| ||| | || || || |
gttttggttttgaattcttgatcttgtccttatatggacaataatccatccaaagttaaatatataggctgaattctttttttttttgtattttttttaaatccacaacagATGGCAAAATATTTTACAGCTTACAGGATTGATCACATATTGGGATTCTTCCGAATTTGGGAACTTCCGGATCATGCTGCGACAGGTCTTGTTGGAAAAT
upper sequence: AT2G40840.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA19G30580.1 (Glycine max), 3'ss of exon 14
-------------gttggaattattgtccttac-cagcca------catcctttgt-agatctgaaggctga-----------ccacattgcatacttgctttg---------cagATGGGGAAATATTTCACAGCATACAGGATTGATCATATATTGGGATTCTTCAGAATCTGGGAGCTTCCAGCTCATGCTATGACTGGTTTAGTGGGGAAGT
|| | ||||||||| | || ||||| || | || | ||||||| | ||| || || ||| ||||||| |||||||| ||||| |||||||||||||| || |||||||||||| |||| ||||| ||||| | ||||||| ||| ||| | || || || |
gttttggttttgaattcttgatcttgtccttatatggacaatagtccatccaaagttaaatatagaggctgaatcttttttatttattttgtattttttttttaaatccacaacagATGGCAAAATATTTTACAGCTTACAGGATTGATCACATTTTGGGATTCTTCCGAATTTGGGAACTTCCGGATCATGCTGCGACAGGTCTTGTTGGAAAAT
upper sequence: AT2G40840.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv08s0040g00670.t01 (Vitis vinifera), 3'ss of exon 12
-----------------------------------gttggaattat-tgtccttaccagccac---atcctttgtag-atctgaaggctga--ccacattgcatacttgctttgcagATGGGGAAATATTTCACAGCATACAGGATTGATCATATATTGGGATTCTTCAGAATCTGGGAGCTTCCAGCTCATGCTATGACTGGTTTAGTGGGGAAGT
|| || ||| ||||| | || || || | |||| |||| | || | || || ||||||| ||||| ||||| || ||||| |||||||||||| |||| ||||| ||||||||||||||||||| ||||||||||| ||| |||| || ||||
gtttcacacttactgtctaaatttttatcctctttgtctactccatctgttcttacattgtattctatgctctggactatctcttttctgaagttaagttttcttttttgttctcagATGGCAAAATACTTCACCGCTTACAGAATTGATCATATACTGGGTTTCTTTAGAATCTGGGAGCTTCCAGAGCATGCTATGACAGGTCTAGTTGGAAAGTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|47831900|gb|CK121584.1|CK121584EST: AGGAAATGTCAAAAGACAACTATGCCTGGTGGCGTGCTCGCCTAACACAG ATGGGGAAATATTTCACAGCATACAGGATTGATCATATATTGGGATTCTTC
genomic: AGGAAATGTCAAAAGACAACTATGCCTGGTGGCGTGCTCGCCTAACACAGgttggaatta ... tgctttgcagATGGGGAAATATTTCACAGCATACAGGATTGATCATATATTGGGATTCTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagccacatcctttgtagatctgaaggctgaccacattgcatacttgctttgcagATGGGGAAATATTTCACAGCATACAGGATTGATCATATATTGGGATTCTTCAGAATCTGGGAGCTTCCAGCTCATGCTATGACTGGTTTAGTGGGGAAGT
ggctgac putative branch site (score: 3)
cttgcttt putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggaattattgtccttaccagccacatcctttgtagatctgaaggctgaccacattgcatacttgctttgcagATGGGGAAATATTTCACAGCATACAGGATTGATCATATATTGGGATTCTTCAGAATCTGGGAGCTTCCAGCTCATGCTATGACTGGTTTAGTGGGGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA