Sequence
atgc intronic sequence ATGC exonic sequencegtataacaaaacgtctaaaactaagcatttgctaatcatatacattttgaaagttggtaatcataccgtgactaaccggaatctatggttttgtggtttaatcaacagCCGGGAACGGTTTGGGGAAGTGCATGCAAAGACATGGTGGGAGCAGAACAGAGAGAGAATACAAACACAGTACCTCTAAGCAAACGAAATATTATGAGTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G31880.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G31880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os04g51172.1 (Oryza sativa), 3'ss of exon 4
gtataacaaaacgtctaaaactaagc---atttgctaatcatatacattttgaaagt---tggtaatcataccgtgactaaccggaatctatggttttgtggtttaatcaacagCCGGGAACGGTTTGGGGAAGTGCATGCAAAGACATGGTGGGAGCAGAACAGAGAGAGAATACAAACACAGTACCTCTAAGCAAACGAAATATTATGAGTA
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-----------ctttcaaatctaaccagaatttcatgtatatactcgcctagggactactttctgattgatccatgcttaatcgtactcaattgattctctgctt---ctgcagCCGCGAGAGGTTTGGTGAGGACAGGGCGAAGGTTTGGTGGGAGCACAACAGAGACAGAATACAAGCACAGTATCTGTAACAAGGCATGCATCTATGCATG
upper sequence: AT1G31880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G374203_T01 (Zea mays), 3'ss of exon 5
--------------------------gtataacaaaacgtctaaaactaagcatttgctaatcata-tacattttgaaagttggtaatcatac-cgtgactaaccggaatctatggttttgtggtttaatcaacagCCGGGAACGGTTTGGGGAAGTGCATGCAAAGACATGGTGGGAGCAGAACAGAGAGAGAATACAAACACAGTACCTCTAAGCAAACGAA-ATATTATGAGTA
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gtatgcatggcactgatcagtcatggacatgcggaagcatacatcactgg---ctcagtaaccaaaatccttcttgatcactcg-gttcattcatgtgatcatgtctgttccatgtttctgtgatg----ctgcagCCGGGAGATATTCGGCGAGGATAGGGCCAAGGTGTGGTGGGAGCAGAACAGGGAGAGAATACAGGCGGAATATCTGTA-GCAAGCGATCAGACACTGAGCT
upper sequence: AT1G31880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G08070.1 (Glycine max), 3'ss of exon 5
gtataacaaaacgtctaaaactaagcatttgctaatcatatacattttgaaagttggtaatcataccgtgactaaccggaatctatggttttgtggtttaatcaacagCCGGGAACGGTTTGGGGAAGTGCATGCAAAGACATGGTGGGAGCAGAACAGAGAGAGAATACAAACACAGTACCTCTAAGCAAACGAAATATTATGAGTA-
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---tgggtcatcacccattttgaagggtgtacaaaagacttttgtgtagactttagatgcatgttaggttttgagttgacactttctctattaatgtttt-----cagCCGGGAAAGATTTGGGGAGGTGAATGCAAAAACTTGGTGGGAAGAGAACAGAGAGAGAATACAAGCTCAATATCTTTGAACTT-TGAAGTCACATTTTCCT
upper sequence: AT1G31880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G17590.1 (Glycine max), 3'ss of exon 3
gtataacaaaacgtctaaaactaagcatttgctaatcatatacattttgaaagttggtaatcataccgtgactaaccggaatctatggttttgtggttta---atcaacagCCGGGAACGGTTTGGGGAAGTGCATGCAAAGACATGGTGGGAGCAGAACAGAGAGAGAATACAAACACAGTACCTCTAAGC----AAACGAAATATTATGAGTA
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------tattaggttttgaa-tgaacactttctcaactaatatttgtttagactttatatgcttatta-gatt---ttgaattaacactttctcaactcttatgtttgcagCCGGGAAAGATTTGGGGAGGTGAATGCAAAAACTTGGTGGGAAGAGAACAGAGAGAGAATCCAAGCTCAATATCTTTGAACTTTGAAGTCAAATTTTTCT----
upper sequence: AT1G31880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv02s0033g00590.t01 (Vitis vinifera), 3'ss of exon 4
gtataacaaaacgtctaaaactaagcatttgcta--atcatatacattttgaaagttggtaatcataccgtgactaaccggaatctatggttttgtggtttaatcaacagCCGGGAACGGTTTGGGGAAGTGCATGCAAAGACATGGTGGGAGCAGAACAGAGAGAGAATACAAACACAGTACCTCTAAGCAAACGAAATATTATGAGTA-
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-------aaagctttaaatgattcgatttttatagcattctgtccatgattgaaatcatt--tcat-tcttcatctatggttgttgatgtcttctctatgatctttacagCCGTGAAAGATTTGGTGAGGTCCATGCAAAGACGTGGTGGGAAGAGAATCGAGAGAGAATACAAGCTCAATACCTCTAAATTTA-GATTTTTCACAAAACTMapped 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|19742062|gb|AU227415.1|AU227415EST: ATCAGACAATTATCAGATGGGACTAGAGAGCTACGTCGAGTCAGATTCAG CCGGGAACGGTTTGGGGAAGTGCATGCAAAGACATGGTGGGAGCAGAACAG
genomic: ATCAGACAATTATCAGATGGGACTAGAGAGCTACGTCGAGTCAGATTCAGgtataacaaa ... taatcaacagCCGGGAACGGTTTGGGGAAGTGCATGCAAAGACATGGTGGGAGCAGAACAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggtaatcataccgtgactaaccggaatctatggttttgtggtttaatcaacagCCGGGAACGGTTTGGGGAAGTGCATGCAAAGACATGGTGGGAGCAGAACAGAGAGAGAATACAAACACAGTACCTCTAAGCAAACGAAATATTATGAGTA
tttaatcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataacaaaacgtctaaaactaagcatttgctaatcatatacattttgaaagttggtaatcataccgtgactaaccggaatctatggttttgtggtttaatcaacagCCGGGAACGGTTTGGGGAAGTGCATGCAAAGACATGGTGGGAGCAGAACAGAGAGAGAATACAAACACAGTACCTCTAAGCAAACGAAATATTATGAGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA