Sequence
atgc intronic sequence ATGC exonic sequencegtaagtacaccattctctatcaccacatccttttcttgagttattcatctgctcttacttaccaaatttttgatcttgcaattgtcgaaacagATTAATATGAAAGGTTTGGATGGATTACAAGGGCCTATATACGTGGGAACCGGGTGTGTTTTTAGGAGACAAGCACTTTATGGATTTGATGCGCCAAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G09870.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G09870.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G15380.1 (Glycine max), 3'ss of exon 10
gtaagtacac-cattctctatcaccacatccttttcttgagttattcatctgctcttacttaccaaatttttgatcttgcaattgtcgaaacagATTAATATGAAAGGTTTGGATGGATTACAAGGGCCTATATACGTGGGAACCGGGTGTGTTTTTAGGAGACAAGCACTTTATGGATTTGATGCGCCAAAAA
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gtaagttttctcttcctctttttttgcttgtttgactgcttttctttcagtcctttaatatggcaa-ctactaactccccaattg--aaaacagATTAACATGAAAGGATTGGATGGGATACAAGGTCCAATATATGTCGGAACTGGATGTGTTTTCAGAAGGTACGCACTTTATGGATATGATGCACCTGCCA
upper sequence: AT5G09870.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G32100.1 (Glycine max), 3'ss of exon 10
gtaagtacaccattctctatcaccacatccttttcttgagttattcatctgctcttacttacca-aatttttgatcttgcaattgtcgaaacagATTAATATGAAAGGTTTGGATGGATTACAAGGGCCTATATACGTGGGAACCGGGTGTGTTTTTAGGAGACAAGCACTTTATGGATTTGATGCGCCAAAAA
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gtaagttttctcttccaattttctttgcttgtttgactgcttttcttttggttctttagtatggcagcttctaactccccaattg--aaaacagATTAACATGAAAGGATTGGATGGGATACAAGGTCCAATATATGTCGGAACGGGATGTGTTTTCAGAAGGTACGCACTTTATGGATATGATGCACCTGCCA
upper sequence: AT5G09870.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv07s0031g02060.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtacaccattctctatcaccacatccttttcttgagttattcatctgctcttacttaccaaatttttgatcttgcaattgtcgaaacagATTAATATGAAAGGTTTGGATGGATTACAAGGGCCTATATACGTGGGAACCGGGTGTGTTTTTAGGAGACAAGCACTTTATGGATTTGATGCGCCAAAAA
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gtatgtatacctttttcttttctt---ttttttccctttattgtt--tcttatatcattgggaaag---ctgatttttcaattg---aaacagATTAACATGAGAGGCTTAGATGGTATACAAGGACCGATATATGTTGGAACCGGTTGTGTCTTCAGAAGGCAAGCACTTTATGGTTATGATGCTCCTGTCAMapped 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|116455074|gb|EG497666.1|EG497666EST: GGATTGATAAAAGTGACAGATACTCTAATCGTAATGTTGTATTCTTCGAT ATTAATATGAAAGGTTTGGATGGATTACAAGGGCCTATATACGTGGGAACC
genomic: GGATTGATAAAAGTGACAGATACTCTAATCGTAATGTTGTATTCTTCGATgtaagtacac ... gtcgaaacagATTAATATGAAAGGTTTGGATGGATTACAAGGGCCTATATACGTGGGAACC
EST:
gi|125176694|gb|EL195995.1|EL195995EST: GTATTCTTCGAT ATTAATATGAAAGGTTTGGATGGATTACAAGGGCCTATATACGTGGGAACC
genomic: GTATTCTTCGATgtaagtacac ... gtcgaaacagATTAATATGAAAGGTTTGGATGGATTACAAGGGCCTATATACGTGGGAACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttattcatctgctcttacttaccaaatttttgatcttgcaattgtcgaaacagATTAATATGAAAGGTTTGGATGGATTACAAGGGCCTATATACGTGGGAACCGGGTGTGTTTTTAGGAGACAAGCACTTTATGGATTTGATGCGCCAAAAA
aaatttttgatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtacaccattctctatcaccacatccttttcttgagttattcatctgctcttacttaccaaatttttgatcttgcaattgtcgaaacagATTAATATGAAAGGTTTGGATGGATTACAAGGGCCTATATACGTGGGAACCGGGTGTGTTTTTAGGAGACAAGCACTTTATGGATTTGATGCGCCAAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA