Sequence
atgc intronic sequence ATGC exonic sequencegtaaagagccccatccaactcttcttttcagttgattcttttacttcactaacactcatagcttaaatagGTGTGGAAGTGTCACCATTGTGCTCGTACGCTGGAGAAAATCTAGAAGCGATTTGTCGGGGAAGAACCTTTCACGCACCATGTGAAATCTCCCTCTAATC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35020.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35020.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 15
-----------------------------------------------------------------------------------------------------------------------gtaaagagccccatc-------caactcttcttttcagttgattcttttacttcact--aacactcatagcttaaatagGTGTGGAAGTGTCACCATTGTGCTCGTACGCTGGAGAAAATCTAGAAGCGATTTGTCGGGGAAGAACCTTTCACGCACCATGTGAAATCTCCCTCTAATC
||| | | | | | | | | | | ||||| || | || | || | |||||| |||||||||||| | || ||||| ||||| ||||| || ||| | || ||||| |||||||| ||||| ||||| ||||| ||||| |||| |
gtaagttatttactctttttttttttcatggagaagaagtataattgcggctggactcttgcacagacatatgtacacacacacatggagagaatgtgacagaaagagatggagagatagtataattttttgttagaaaagtgattgtcttatctaactcttccttttctttttatggaatgtcccgccctcattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCAATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCGTTCTAGTT
upper sequence: AT2G35020.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 14
----------------------------------------------------------------------------------------------------------------------gtaaagagccccatccaactcttcttttcagttgattcttttactt--cactaacactcatagc--ttaaatagGTGTGGAAGTGTCACCATTGTGCTCGTACGCTGGAGAAAATCTAGAAGCGATTTGTCGGGGAAGAACCTTTCACGCACCATGTGAAATCTCCCTCTAATC
|| | || | | | | | | | |||||| ||| || || || || ||| |||||| |||||||||||| | || ||||| ||||| ||||| || ||| | || ||||| |||||||| ||||| ||||| ||||| ||||| | || |
gtaggttatttactctttatttccaaggagaagaaatatagttgcggccggactcttacccagacatatgtatacacacatggagagaatatgtgacataaatagatggagagatagtatattttttgttagaaaaatgatggtcttatctaactctttttcttttcatgaaatgtccctgcccttattcagGTGTTGAAGTGTCACCACTCTGTTCGTATGCTGGTGAAAACCTGGAACCTATATGTCGAGGAAGAACATTTCATGCACCTTGTGAGATCTCATTTTAGTT
upper sequence: AT2G35020.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 14
--------------------------------gtaaagagccccatccaactcttcttttcagttgattcttttacttcactaacactcatagcttaaatagGTGTGGAAGTGTCACCATTGTGCTCGTACGCTGGAGAAAATCTAGAAGCGATTTGTCGGGGAAGAACCTTTCACGCACCATGTGAAATCTCCCTCTAATC
| | || | | | |||| | || | | ||||| | | | | | || ||||||||| | |||||| | ||||| || |||| ||||| |||||||| || || || |||||||| |||||||| || ||||||||||| ||||
ataaatcatacataattcttctcattttcaatggtagtggcactaacagactcatattct-atttgata-tgtggtgtggcggtgtttgatgtggaggccagGTGTGGAGATATCACCACTCTGCTCCTATTCTGGGGAAAACCTAGAAGCCATCTGCCGTGGAAGAACATTTCACGCTCCTTGTGAAATCTCATTCTAGAGMapped 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|124954189|gb|EL029305.1|EL029305EST: CATAGCAGCTGGTGGATTTCTAACACATTCCGTTCCTTTATATGCGACTG GTGTGGAAGTGTCACCATTG
genomic: CATAGCAGCTGGTGGATTTCTAACACATTCCGTTCCTTTATATGCGACTGgtaaagagcc ... gcttaaatagGTGTGGAAGTGTCACCATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caactcttcttttcagttgattcttttacttcactaacactcatagcttaaatagGTGTGGAAGTGTCACCATTGTGCTCGTACGCTGGAGAAAATCTAGAAGCGATTTGTCGGGGAAGAACCTTTCACGCACCATGTGAAATCTCCCTCTAATC
cactaac putative branch site (score: 1)
attctttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagagccccatccaactcttcttttcagttgattcttttacttcactaacactcatagcttaaatagGTGTGGAAGTGTCACCATTGTGCTCGTACGCTGGAGAAAATCTAGAAGCGATTTGTCGGGGAAGAACCTTTCACGCACCATGTGAAATCTCCCTCTAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC