Sequence
atgc intronic sequence ATGC exonic sequencegtggttcttttccaagacatatacacctctaaagccgtgctcttttctaaccatcatataaaatctttgtgattgtgtagATAAGTTTCGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCTCTTGCAGTGCCGGATGAAGACAACTGTATGGTGGTTTATAGCTCGACTCAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G20960.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G04950.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------gtggttcttttccaagacatatacacctctaaagccgtgctct----tttctaaccatcatataaaatctttgtgatt--gtgtagATAAGTTTCGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCTCTTGCAGTGCCGGATGAAGACAACTGTATGGTGGTTTATAGCTCGACTCAAA
||| | | | || | | | |||| | || | | || || || || || || || | | | ||||| || |||| |||||||||||||||||||| || ||||| || || ||||||||||| || || ||||| ||| | |||
gtacattgtttactttgcttcccctcttcctctcattccatacctttgtgaaccttggtttctgatacaatgtttaagtttgctcctgaataattaatgtttaattggttatgctgaacaaatactcattgttatctatcatattcaatgttaaatgcagTTGAAACTTGGGTCTCAATACTATTTCTATATGGAGACACAAACTGCACTTGCTGTTCCAGATGAAGACAATTGCATTACAGTTTACTCCTCAAACCAAT
upper sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0041g02410.t01 (Vitis vinifera), 3'ss of exon 4
-----------gtggttcttttccaagacatatacacctctaaagccgtgctcttttctaaccatcat------ataaaatctttgtgatt------gtgtagATAAGTTTCGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCTCTTGCAGTGCCGGATGAAGACAACTGTATGGTGGTTTATAGCTCGACTCAAA
| || || | ||| | | | ||| || | ||||| | | ||||| |||| ||| | | |||| || | ||||||||||| | |||||||||||||||||||| || |||||||| || |||||||||||||| || |||||||| || || | |||
gtacttctcatttacttgttatacaatttttttctattcctattaatgtttttctttcttgttttggttttatgataaatgctttctgaattgtcacatccagATCAGACTTGGGTCACAGTATTATTTCTATATGGAGACACAAACTGCCCTTGCAGTTCCCGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
upper sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0041g02430.t01 (Vitis vinifera), 3'ss of exon 4
----------------------gtggttcttttccaagacatatacacctctaaagccgtgctcttttctaaccatcatataaaatctttgtgatt------gtgtagATAAGTTTCGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCTCTTGCAGTGCCGGATGAAGACAACTGTATGGTGGTTTATAGCTCGACTCAAA
|| |||| | | | ||| | | | | || || | | ||||| |||| ||| | | |||| || | ||||||||||| | |||||||||||||||||||| || |||||| | ||||||||||||||||| || |||||||| || || | ||
gtacttctcatttacttgttatacaattttttttctattcctattaatgttt----ttctttcctgttttggttttatgataaatgctttctgaattgtcacatccagATCAGACTTGGGTCACAGTATTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCGGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAGT
upper sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0041g02390.t01 (Vitis vinifera), 3'ss of exon 3
----------------------gtggttcttttccaagacatatacacctctaaagccgtgctcttttctaaccatcatataaaatctttgtgatt------gtgtagATAAGTTTCGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCTCTTGCAGTGCCGGATGAAGACAACTGTATGGTGGTTTATAGCTCGACTCAAA
| || |||||| | |||| | | || | ||||||| | | ||||| |||| | | | | |||| | | |||||||| || | ||||||||||||||| ||||| || |||||||| || |||||||| ||||| || |||||||| || | | |||
gtacttctcatttacttgttatgcaatttttttcctatttatattatttttt---tcctttctctttt-tggttttatgataaatactttctaaattgtcacatccagATCAAACTTGGGTCACAATATTACTTCTATATGGAGACCCAAACTGCCCTTGCAGTTCCAGATGAAGATAACTGCATTGTGGTTTACAGTGCAATACAAT
upper sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------gtggttcttttccaagacatatacacctctaaagccgtgctcttttc-taaccatcatataaaatctttgtgattgtgtagATAAGTTTCGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCTCTTGCAGTGCCGGATGAAGACAACTGTATGGTGGTTTATAGCTCGACTCAAA
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gtatttgtcatttacttgttatacaaattttgttcctatttctattagtgtttttcttttattttttggttttgtgatgaataat-tgctgaattgtcctcat-gtccagATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAATMapped 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|116484492|gb|EG527084.1|EG527084EST: ATATCACCAAGGGAATGGATGAAGCTGAACATAAGATTCTTGGATCAAAG ATAAGTTTCGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCTCTT
genomic: ATATCACCAAGGGAATGGATGAAGCTGAACATAAGATTCTTGGATCAAAGgtggttcttt ... gattgtgtagATAAGTTTCGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCTCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctctaaagccgtgctcttttctaaccatcatataaaatctttgtgattgtgtagATAAGTTTCGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCTCTTGCAGTGCCGGATGAAGACAACTGTATGGTGGTTTATAGCTCGACTCAAA
ttctaac putative branch site (score: 1)
atcatataaaatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggttcttttccaagacatatacacctctaaagccgtgctcttttctaaccatcatataaaatctttgtgattgtgtagATAAGTTTCGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCTCTTGCAGTGCCGGATGAAGACAACTGTATGGTGGTTTATAGCTCGACTCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG