Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttcatcatatacatcttctgtaagattacttctcatgtaattgtgttctgtttaatcatcttatcttgctaatggtttatgcagGACTAATGTGTGAACTATTGTGGAGTGATCCTCAACCTCTCCCTGGAAGAGGCCCAAGCAAGCGAGGAGTTGGTCTATCATTTGGTGGAGATGTGACAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G42810.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 9
-----gtatgtttcatcatatacatcttctgtaagattacttctcatgtaattgtgttctgtttaatcatct--tatcttgctaatggtttatgc----agGACTAATGTGTGAACTATTGTGGAGTGATCCTCAACCTCTCCCTGGAAGAGGCCCAAGCAAGCGAGGAGTTGGTCTATCATTTGGTGGAGATGTGACAAA
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aaccattaatttgcattataagtgttggc-atattatttaccttgatgccttttttcccatgttagttatctgccaacatgactcctgtttctgctgacagGTCTAATGTGTGAAGTATTATGGAGTGATCCTCAGCCTCAACTTGGTAGAGGTCCAAGCAAACGCGGTGTTGGTCTTTCGTTTGGTGCAGATGTGACTAA
upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G126435_T02 (Zea mays), 3'ss of exon 8
--------gtatgtttcatcatatacatcttctgtaagatt--acttctcatgtaattgtgttctgtttaatcatcttatcttgctaatggtttatgcagGACTAATGTGTGAACTATTGTGGAGTGATCCTCAACCTCTCCCTGGAAGAGGCCCAAGCAAGCGAGGAGTTGGTCTATCATTTGGTGGAGATGTGACAAA
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cccaccactcagatttcaggatgtatgatgatggcatctttccattgtctacttagcaatgatggcatatgacacaacgtggtgttgctctttatggcagGTCTAATGTGTGAATTACTATGGAGTGACCCTCAGCCTCAGCTTGGAAGAGGTCCAAGTAAACGTGGTGTTGCTCTTTCCTTTGGCGCAGATGTGACTAA
upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G12440.1 (Glycine max), 3'ss of exon 9
-------------------------------------------------------------------gtatgtttcat-catatacatcttctgtaagattacttctcatgtaattgtgttctgtttaatcatcttatcttgctaa---tggtttatgcagGACTAATGTGTGAACTATTGTGGAGTGATCCTCAACCTCTCCCTGGAAGAGGCCCAAGCAAGCGAGGAGTTGGTCTATCATTTGGTGGAGATGTGACAAA-
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ttagataaatccttttttgttgtctctaattgatctcccagttatctgcacatatctaaatccctctaaaccttccattcttgcacttcatagactaaacc-cctctggctttttcacccttagtattttagttttatttacctatgtttggtatgtgtaggGTTGATGTGTGAATTGCTCTGGAGTGATCCACAACCTCTCCCTGGAAGGGGCCCAAGCAAGCGTGGTGTAGGCCTTTCTTTTGGTGCAGATGTTACAAAA
upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 9
------------------------------------------------------------------gtatgtttcatcatatacatcttctgtaagattacttctcatgtaattgtgttctgtttaatcatcttatcttgcta---atggtttatgcagGACTAATGTGTGAACTATTGTGGAGTGATCCTCAACCTCTCCCTGGAAGAGGCCCAAGCAAGCGAGGAGTTGGTCTATCATTTGGTGGAGATGTGACAAA
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gttagatacatccttttttgttgtctctaattgatctcccagttaaccacacatacctaaatccctctaaacttt-ccattcttgcactacatagactcacctttggctttttcaccctcagtattgtagttttatgtacctatgtttggtatgtgtagGGTTGATGTGTGAATTGCTATGGAGCGATCCACAACCTCTCCCTGGAAGGGGCCCAAGTAAGCGTGGTGTAGGCCTTTCTTTTGGTGCAGATGTTACAAA
upper sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 3
-----------gtatgtttcatcatatacatcttctgtaagattacttctcatgta-attgtgttctgtttaatcatcttatcttgctaatggtttatgcagGACTAATGTGTGAACTATTGTGGAGTGATCCTCAACCTCTCCCTGGAAGAGGCCCAAGCAAGCGAGGAGTTGGTCTATCATTTGGTGGAGATGTGACAAA
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tttttatgtaagatcattctaaggcatg-atcctctgcttcttcactgcttatgtttattgattactaagtacctttaatatttatctggtattccata-agGATTGATGTGTGAACTGCTGTGGAGTGATCCCCAACCTTACCCTGGAAGAGGCCCTAGCAAGCGGGGTGTAGGTCTTTCCTTTGGTGTAGATGTGACAAAMapped 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|124990815|gb|EL063084.1|EL063084EST: ACTCTCAGACATCAGAGCCATTGACAGATTCTGTGAGCCACCAGAGGAAG GACTAATGTGTGAACTATTGTGG
genomic: ACTCTCAGACATCAGAGCCATTGACAGATTCTGTGAGCCACCAGAGGAAGgtatgtttca ... gtttatgcagGACTAATGTGTGAACTATTGTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctcatgtaattgtgttctgtttaatcatcttatcttgctaatggtttatgcagGACTAATGTGTGAACTATTGTGGAGTGATCCTCAACCTCTCCCTGGAAGAGGCCCAAGCAAGCGAGGAGTTGGTCTATCATTTGGTGGAGATGTGACAAA
tgctaat putative branch site (score: 2)
tttaatcatcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttcatcatatacatcttctgtaagattacttctcatgtaattgtgttctgtttaatcatcttatcttgctaatggtttatgcagGACTAATGTGTGAACTATTGTGGAGTGATCCTCAACCTCTCCCTGGAAGAGGCCCAAGCAAGCGAGGAGTTGGTCTATCATTTGGTGGAGATGTGACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG