Sequence
atgc intronic sequence ATGC exonic sequence...accacacacgcttcaagttcttttaatattctggttatgattaagatttaatcttaagtgttgaagatggtgttaaaggatctattgttctgttttgcagAGAACTTGCTTTTAACTGCAGACCATAAAACAGTAAAACTAGCAGATTTTGGATTAGCAAGAGAAGAGTCACTGACTGAGATGATGACGGCTGAGACAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50180.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 4
accacacacgcttcaagttcttttaatattctggttatgattaagatttaatcttaagtgttgaagatggtgttaaaggatctattgttctgtttt---------gcagAGAACTTGCTTTTAACTGCAGACCATAAAACAGTAAAACTAGCAGATTTTGGATTAGCAAGAGAAGAGTCACTGACTGAGATGATGACGGCTGAGACAGG
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------tttcttttcagagctatt--tttttgaaaaaaaatcaagccagaaatatttgtac-aaataaggtttatcatgagccattgttttgtccttctgtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
upper sequence: AT5G50180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G165231_T01 (Zea mays), 3'ss of exon 3
-accacacacgcttcaagt--tcttttaatattctggttatgattaagatttaatcttaagtgttgaagatggtgttaaaggatctattgttctgttttgcagAGAACTTGCTTTTAACTGCAGACCATAAAACAGTAAAACTAGCAGATTTTGGATTAGCAAGAGAAGAGTCACTGACTGAGATGATGACGGCTGAGACAGG
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aatttttttcgtcccatgtcatcttttaagaatctaccg--gacagatatctattca-gactgatgatcttgagtccgtgttttcccccttcatttcgtgcagAGAATCTGTTGCTGACTGCAGACCAGAGAACAGTAAAACTTGTTGATCTTGGTTTGGCTAGGGAAGAGACACTAACGGAGATGATGACTGCTGAGACAGG
upper sequence: AT5G50180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G36210.1 (Glycine max), 3'ss of exon 3
accacacacgcttcaagttcttttaatattctggttatgattaagatttaatcttaagtgttgaagatggtgttaaaggatctattgttctgtttt--gcagAGAACTTGCTTTTAACTGCAGACCATAAAACAGTAAAACTAGCAGATTTTGGATTAGCAAGAGAAGAGTCACTGACTGAGATGATGACGGCTGAGACAGG
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-agttgttaacttaagcttctttttctcctttgtata-acttgccaaagtgtcaaacatctacataatgaatatgaagatccttttattttcctctatacagATAACTTGCTATTGACTGAAGACCAGAAAACAGTCAAGCTAGCAGATTTTGGTTTAGCAAGAGAAGAGTCATTAACTGAGATGATGACTGCTGAAACAGG
upper sequence: AT5G50180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G18730.1 (Glycine max), 3'ss of exon 3
accacacacgcttcaagttcttttaatattctggttatgattaagatttaatcttaagtgttga-agatggtgttaaaggatctattg---ttctgttttgcagAGAACTTGCTTTTAACTGCAGACCATAAAACAGTAAAACTAGCAGATTTTGGATTAGCAAGAGAAGAGTCACTGACTGAGATGATGACGGCTGAGACAGG
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-ttgttcagtatatacgcattttttatcaattg--tataactc-gcccaagtgtaaaacatcaacataatgtatatgaggatccttttattttcctctatacagATAACTTGCTATTGACTGAAGACCAGAAAACAGTCAAGCTAGCGGATTTTGGTTTAGCAAGAGAAGAGTCATTAACTGAGATGATGACTGCTGAGACGGGMapped 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|164232476|gb|EL990860.1|EL990860EST: CTTGCATTCCCATGGGATCATTCACCGTGATCTCAAACCCG AGAACTTGCTTTTAACTGCAGACCATAAAACAGTAAAACTAGCAGATTTTG
genomic: CTTGCATTCCCATGGGATCATTCACCGTGATCTCAAACCCGgtaaaactac ... tgttttgcagAGAACTTGCTTTTAACTGCAGACCATAAAACAGTAAAACTAGCAGATTTTG
EST:
gi|86054523|gb|DR350280.1|DR350280EST: TATGGAATGCTTGCATTCCCATGGGATCATTCACCGTGATCTCAAACCCG AGAACTTGCTTTTAACTGCAGACCATAAAACAGTAAAACTAGCAGATTTTG
genomic: TATGGAATGCTTGCATTCCCATGGGATCATTCACCGTGATCTCAAACCCGgtaaaactac ... tgttttgcagAGAACTTGCTTTTAACTGCAGACCATAAAACAGTAAAACTAGCAGATTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttaatcttaagtgttgaagatggtgttaaaggatctattgttctgttttgcagAGAACTTGCTTTTAACTGCAGACCATAAAACAGTAAAACTAGCAGATTTTGGATTAGCAAGAGAAGAGTCACTGACTGAGATGATGACGGCTGAGACAGG
atttaat putative branch site (score: 4)
ttctgtttt putative PPT
atcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accacacacgcttcaagttcttttaatattctggttatgattaagatttaatcttaagtgttgaagatggtgttaaaggatctattgttctgttttgcagAGAACTTGCTTTTAACTGCAGACCATAAAACAGTAAAACTAGCAGATTTTGGATTAGCAAGAGAAGAGTCACTGACTGAGATGATGACGGCTGAGACAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- cacacac