Sequence
atgc intronic sequence ATGC exonic sequencegtaaatcatactctctcaagcctaattagtgcaacatttcttgcctacttacctctgactcatctattaatacagaaaaatgcagtctttttccataaatactcttcctttttattggtaattttttgtgtattcaagtaagtatccacatttttttcagGCATTGTTGGTCGGATATCCCCCAAAACATGGGCTGCTATGGAAGTATTTTTAGCGTCTATTGCAACTGAAGAATATGAATCCATGGCCTCAGCTTTGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G05200.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G05200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G031780_T02 (Zea mays), 3'ss of exon 6
gtaaatcatactctctcaagcctaattagtgcaacatttcttgcctacttacctctgactcatctattaatacagaaaaatgcagtctttttccataaatactcttcctttttattggtaattttttgtgtattcaagtaagtatccacatttttttcagGCATTGTTGGTCGGATATCCCCCAAAACATGGGCTGCTATGGAAGTATTTTTAGCGTCTATTGCAACTGAAGAATATGAATCCATGGCCTCAGCTTTGAT
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---------------------------------------------------------ttatacacaaaagttccaaacattctaggttgattacagtatcattatagtttgtgattggaacttttgcata-ataattgtactaattaacacttct--cagGGATTGTTGGTCGAATATCTCCAAGAACTTGGGCAGCTATGGAGGTCTTTTTGGCTTCTTTTGCAACTGAGGATTATGATGCTATGGCCTCTGCCCTCTC
upper sequence: AT5G05200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA14G36520.1 (Glycine max), 3'ss of exon 7
gtaaatcatactctctcaagcctaattagtgcaacatttcttgcctacttacctctgactcatctattaatacagaaaaatgcagtctttttccataaatactcttcctttttattggtaattttttgtgtattcaagta--agtatccacattt--ttttcagGCATTGTTGGTCGGATATCCCCCAAAACATGGGCTGCTATGGAAGTATTTTTAGCGTCTATTGCAACTGAAGAATATGAATCCATGGCCTCAGCTTTGAT
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---------------------------------------------------------agacaccatttcttttctaaaaactaaatgttttacagta-------ttcagttatatgtatgagattttgtgaatctaaattctattaaaaaaattcgatctacagGAATTGTTGGTCGTATATCCCCTAAAACATGGGCTGCTATGGAAGTCTTCTTAGGATCAATTGCCATTGAAGATTATGACTCAATGGCATCTTCCTTAAT
upper sequence: AT5G05200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv13s0067g03210.t01 (Vitis vinifera), 3'ss of exon 8
gtaaatcatactctctcaagcctaattagtgcaacatttcttgcctacttacctctgactcatctattaatacagaaaaatgcagtctttttccataaatactcttcctttttattggtaattttttgtgtattcaagtaagtatccacattttttt-cagGCATTGTTGGTCGGATATCCCCCAAAACATGGGCTGCTATGGAAGTATTTTTAGCGTCTATTGCAACTGAAGAATATGAATCCATGGCCTCAGCTTTGAT
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-------------------------------------------------------------ctgtataaacacttttgaactggttccatggtcattgctattcagtacccatgcatgaaagcaatgttgcatatatttaaatttcaattttaatttacagGAATTGTTGGACGCATATCCCCAAAAACATGGGCTGCTATGGAAGTCTTTTTGGAATCAATTGCAACCGAAGAGTATGAGTCAATGGCATCTGCTTTAATMapped 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|125117587|gb|EL166670.1|EL166670EST: GGAAACTTATGGCTGTTGCGTGATGGCCGGATTGGGTTTCTTAGATTTTG GCATTGTTGGTCGGATATCCCCCAAAA
genomic: GGAAACTTATGGCTGTTGCGTGATGGCCGGATTGGGTTTCTT-GATTTTGgtaaatcata ... tttttttcagGCATTGTTGGTCGGATATCCCCCAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctttttattggtaattttttgtgtattcaagtaagtatccacatttttttcagGCATTGTTGGTCGGATATCCCCCAAAACATGGGCTGCTATGGAAGTATTTTTAGCGTCTATTGCAACTGAAGAATATGAATCCATGGCCTCAGCTTTGAT
tccacatttttttc CT-rich tract
tttattggtaattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatcatactctctcaagcctaattagtgcaacatttcttgcctacttacctctgactcatctattaatacagaaaaatgcagtctttttccataaatactcttcctttttattggtaattttttgtgtattcaagtaagtatccacatttttttcagGCATTGTTGGTCGGATATCCCCCAAAACATGGGCTGCTATGGAAGTATTTTTAGCGTCTATTGCAACTGAAGAATATGAATCCATGGCCTCAGCTTTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT