Sequence
atgc intronic sequence ATGC exonic sequencegttagtttacaatgcacatgtctatatcatattctttaagtccaagcataaccatttacttataggaaagccttttatgctgcagATATTCTTATATGGTGGTTATTCAAAAGAAGTCTCATCCGAGAAGAGCTCTGAGAAAGGAATTGTTCATGCAGATTTGTGGTCTCTTGATCCCAGGACTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50310.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G100815_T01 (Zea mays), 3'ss of exon 6
---------------gttagtttacaatgcacatgtctatatcatattctttaagt-ccaagcataaccatttacttataggaaagccttttatgctgcagATATTCTTATATGGTGGTTATTCAAAAGAAGTCTCATCCGAGAAGAGCTCTGAGAAAGGAATTGTTCATGCAGATTTGTGGTCTCTTGATCCCAGGACTT------
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aaattatggtcttatggcacatta-gatgccaagaactattggttatgccttgttttcttactagttttatttgcaaatgtctttatgttcttttttgcagATATATCTATATGGTGGATATTTTAAAGAAGTTTCTTCTGACAAA------GAAAAAGGAACAGTTCATGCAGATATGTGGTCTCTTGATCCTCGTACTTGGGAGT
upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 9
-----------------gttagtttacaatgcacatgtctatatcatattctttaagtccaagcataaccatttacttataggaaagccttttatgctgcagATATTCTTATATGGTGGTTATTCAAAAGAAGTCTCATCCGAGAAGAG---CTCTGAGAAAGGAATTGTTCATGCAGATTTGTGGTCTCTTGATCCCAGGACTT
|| | ||| || |||| | || | || |||| || | | | | |||| || ||||| | ||||||| || || |||||||| |||||||||||||| ||||| || ||||| |||||||||||||||||||||| ||||| ||||||| |||||||| | |
gttttcctctatgtactgtatgattaatttgtgtggctctacaaagtagttttgaagttcag--aatattgtcttcttaagagagttcctttcacattgcagATTTTTTTGTATGGTGGCTATTCAAAAGAAGTTTCATCTGATAAGAGCAACTCTGAGAAAGGAATTGTTCATTCAGATATGTGGTCCCTTGATCCTAAAA---
upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G18170.1 (Glycine max), 3'ss of exon 9
---------------gttagtttacaatgcacatgtctatatcatattctttaagtcca-agcataaccatttacttataggaaagccttttatgctgcagATATTCTTATATGGTGGTTATTCAAAAGAAGTCTCATCCGAGAAGAG---CTCTGAGAAAGGAATTGTTCATGCAGATTTGTGGTCTCTTGATCCCAGGACTT
|| || | | | | | || ||| || | | || || | || || | | | ||||| | ||||||| || || |||||||| ||||| |||||||| ||||| || ||||| |||||||||||||||||||||| ||||| ||||||| |||||||| | |
ttcattatgtttattactatagtaaagttttcccctatgtactgtatgattaatttgtgtggctctacaaagtagtttt-gaagttcctttcaccttgcagATTTTTTTGTATGGTGGCTATTCGAAAGAAGTTTCATCTGATAAGAGCAACTCTGAGAAAGGAATTGTTCATTCAGATATGTGGTCCCTTGATCCTAAGT---Mapped 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|124885966|gb|EH964868.1|EH964868EST: GCTAGAAGTGGCTTCCAGTTTTTTGTTTATCAAGATGAG ATATTCTTATATGGTGGTTATTCAAAAGAAGTCTCATCCGAGAAGAGCTCT
genomic: GCTAGAAGTGGCTTCCAGTTTTTTGTTTATCAAGATGAGgttagtttac ... tatgctgcagATATTCTTATATGGTGGTTATTCAAAAGAAGTCTCATCCGAGAAGAGCTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctttaagtccaagcataaccatttacttataggaaagccttttatgctgcagATATTCTTATATGGTGGTTATTCAAAAGAAGTCTCATCCGAGAAGAGCTCTGAGAAAGGAATTGTTCATGCAGATTTGTGGTCTCTTGATCCCAGGACTT
gcataac putative branch site (score: 3)
ccttttat putative PPT
atttacttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttacaatgcacatgtctatatcatattctttaagtccaagcataaccatttacttataggaaagccttttatgctgcagATATTCTTATATGGTGGTTATTCAAAAGAAGTCTCATCCGAGAAGAGCTCTGAGAAAGGAATTGTTCATGCAGATTTGTGGTCTCTTGATCCCAGGACTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT