Sequence
atgc intronic sequence ATGC exonic sequencegtaggagtaaacacttatcagcttttaattctcaacttatctgcgtgtcaattcacattcttataacttggtttctattatgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G46440.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
--------------gtaggagtaaacacttatcagcttttaattctc--aacttatctg-cgtgtcaattcacattcttataacttggtttctattatgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
| | | | | |||| ||||| || || || |||||| | || | ||| | |||| || || | || | |||||||||||| ||||||||||| || |||||||| |||||||| |||||||||||||| |||| ||| ||||| ||||
gtaaatttgttcatctgaaatttgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttat---ttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 8
--------------gtaggagtaaacacttatcagcttttaattctc--aacttatctg-cgtgtcaattcacattcttataacttggtttctattatgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
| | | | | |||| ||||| || || || |||||| | || | ||| | || | || || | || | |||||||||||| ||||||||||| || |||||||| || |||| |||||||||||||| |||||||| ||||| ||||
gtaaatttcttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttt--atttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTG
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 7
--------------gtaggagtaaacacttatcagcttttaattctc--aacttatctg-cgtgtcaattcacattcttataacttggtttctattatgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
| | | | | |||| ||||| || || || |||||| | || | ||| | || | || || | || | |||||||||||| ||||||||||| || |||||||| || |||| |||||||||||||| |||||||| ||||| ||||
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttt--atttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTG
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
--------------gtaggagtaaacacttatcagcttttaattctc--aacttatctg-cgtgtcaattcacattcttataacttggtttctattatgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
| | | | | |||| ||||| || || || |||||| | || | ||| | || | || || | || | |||||||||||| ||||||||||| || |||||||| || ||||| ||||||| ||||| |||||||| ||||| ||||
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttacaattttt--atttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 7
--------------gtaggagtaaacacttatcagcttttaattct-caacttatc-tgcgtgtcaattcacattcttataacttggtttctattatgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
| | | | ||| ||||| | || || ||||| | | || | | || | || | ||| ||| | ||| ||| || ||||||||||||||||| || |||||||| || ||||| ||||||| ||||| |||||||| ||||| ||||
gtaaatttgttcatctgacaattgcaatatatttgctttgattttcataaattatcattcaagttatcttacggttttg--atttgattttttctat--cagGAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 4
--------------gtaggagtaaacacttatcagcttttaattctca--acttatctg-cgtgtcaattcacattcttataacttggtttctattatgatagGTGTT-AGGAGCTGTTATGATGAAGGCAAGCGTGTTGCT-GAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
| | | | |||| ||||| || ||| | |||||| | || | ||| | || || | ||| | ||| |||||||| ||||| ||||||||||| || |||||||| || ||||| |||||||| ||||| |||||||| ||||| ||||
gtaaatttgttcatctgaacattgaaaattatttgctttggtttttcataaattatctttcaagttctcttacagtttt-tatttaacttttttctat--tagGTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTG
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
gtaggagtaaacacttatca--gcttttaattctcaacttatctgcgtgtc----aat-tcacattctta-taacttggtttc-----tat-tatga-tagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
||||| | | | | || | |||||| | | |||| | || ||| | | || | | || | | ||| ||||| ||| ||| |||| ||||||||||| |||||||||||||| || || ||||||||||| || || ||||| |||||||| |
-taggaatttggaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
-------gtaggagtaaacacttatcagcttttaattctcaacttatctgcgtgtcaattcacattctt--ataacttggtttctattatg-----atagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
| | | || | || | | | | | | | | | || | | | || | ||| | | | ||| | ||| ||| |||| ||||||||||| |||||||||||||| || || ||||||||||| || || ||||| || ||||| |
aatgatcatcgactttaatatataccttatctgtccttttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G04500.1 (Glycine max), 3'ss of exon 8
------------------------gtaggagtaaacacttat---cagcttttaattctcaa--cttatctgcgtgtcaattcacatt----cttataacttggtttct--attatgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
| || | ||||| || || |||| | || | | | | | ||| | || || | |||| | || || ||| ||| | || || |||||||| || || || || |||||||| ||||||||||| ||||| ||||| ||||||||||
gtagattccttcatttcattctcaacttgctaaagcgcttataataaggaactatttctgtatctttttatacatattaataaagatgtagactgaggacttaaatatatgataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTG
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
-gtaggagtaaacacttatcagcttttaattctca-acttatctg-------cgtgtcaattca-cattcttat--aacttggtttctatta--tgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
|| || | | || ||| || | | || | ||| || |||| | || || | || | || || || | | |||||| ||||||| |||||||| || |||||||| |||||||| ||||||||||| || || ||||||||||| || |
aatactgttactcttctttctcttttaaaattgaagacatgtcttgagaaattatgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG
upper sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------gtaggagtaaacacttatcagctttt-aattctca-acttatctgcgtgtcaattcacattcttataac-ttggtttctattatg-atagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
| | | | | || ||| || | || ||| | || | || | ||| |||| ||| || | | || |||| || || ||||| ||||| || || ||||||||||||||||| | |||||||||||||| ||||| ||||| |||
gtaaatccaactcacgttacacgcttggtgcaccatcacgctctgtgcagtttctgaactctgatacacaatcattctacacaaaatattaccttaacgttgcttcttgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGMapped 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|164050517|gb|ES196746.1|ES196746EST: ATGTCAACCCAATTG GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGT
genomic: ATGTCAACCCAATTGgtaggagtaa ... attatgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGT
EST:
gi|47831999|gb|CK121683.1|CK121683EST: TCTCATTCATCCCCAGCCTGAGAGCTATTGGGGAAATGTCAACCCAATTG GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGT
genomic: TCTCATTCATCCCCAGCCTGAGAGCTATTGGGGAAATGTCAACCCAATTGgtaggagtaa ... attatgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaacttatctgcgtgtcaattcacattcttataacttggtttctattatgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
ttataac putative branch site (score: 2)
tttctatt putative PPT
tttctattatgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggagtaaacacttatcagcttttaattctcaacttatctgcgtgtcaattcacattcttataacttggtttctattatgatagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA