Sequence
atgc intronic sequence ATGC exonic sequenceGACCGGTAATGACGAAATTTACAATTGCGTTGAGGGAAATTGGGACTTATAAGGAAGTTCTTCGGTCACAGgtatgctagtttgctattttgacactctctgtttctccctattcccagccttctctctgataactcctgtggtatcaacgtaggatagctttgttttcct...
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13300.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 5'ss of exon 4
GACCGGTAATGACGAAATTTACAATTGCGTTGAGGGAAATTGGGACTTATAAGGAAGTTCTTCGGTCACAGgtatgc---------tagtttgctattttgacactctctgtttctccctattcccagccttctctctgataactcctgtggtatcaacgtaggatagctttgttttcct
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GACCCGTCATGACCAAATTTACAATTGCCCTGAGAGAAATTGGAACTTACAAGGAAGTATTGCGCTCACAGgtaaacattcatatatacattactatacatgcattctct-cttctggaaaatctgaaa-ttctgaatgttcttttctaagttgtcactctttcaga-tattgt------
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM5G872204_T02 (Zea mays), 5'ss of exon 4
GACCGGTAATGACGAAATTTACAATTGCGTTGAGGGAAATTGGGACTTATAAGGAAGTTCTTCGGTCACAGgtatgctagtttgctattt--tgacactctctgtttctccctattcccagccttctctctgataactcctgtggtatcaacgtaggatagctttgttttcct
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GGCCTGTAATGACCAAATTTACAATTGCCTTAAGAGAAATTGGAACATACAAGGAAGTCCTGCGCTCCCAGgtagtgcatttcattttaaaatgtgattatatgtattacctgggccaaattcttgttttccctca-taatgagatgcttatagaaggaaggcctgaaagtg-
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM5G872204_T01 (Zea mays), 5'ss of exon 1
-----------------------------GACCGGTAATGACGAAATTTACAATTGCGTTGAGGGAAATTGGGACTTATAAGGAAGTTCTTCGGTCACAGgtatgctagtttgctattt--tgacactctctgtttctccctattcccagccttctctctgataactcctgtggtatcaacgtaggatagctttgttttcct
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AGCATACTGAATTTTCATCTTCTTTCCAGGGCCTGTAATGACCAAATTTACAATTGCCTTAAGAGAAATTGGAACATACAAGGAAGTCCTGCGCTCCCAGgtagtgcatttcattttaaaatgtgattatatgtattacctgggccaaattcttgttttccctca-taatgagatgcttatagaaggaaggcctgaaagtg-
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA18G51810.1 (Glycine max), 5'ss of exon 4
GACCGGTAATGACGAAATTTACAATTGCGTTGAGGGAAATTGGGACTTATAAGGAAGTTCTTCGGTCACAGgtatgctagtttgctattttgacactctctgtttctccctattcccagccttctctctgataactcctgtggtatcaacgtaggatagctttgttttcct---
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GCCCTGTTATGACCAAATTCACCATAGCCTTAAGAGAAATTGGGACATATAAGGAAGTCCTTCGATCACAGgtaaaccattgtgttgtacttgtaagtgcttttttaatacttctctag--ttgttactgactcctaatgatgcattttt-taagagagatgtaaagtggatga
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 5'ss of exon 4
GACCGGTAATGACGAAATTTACAATTGCGTTGAGGGAAATTGGGACTTATAAGGAAGTTCTTCGGTCACAGgtat-gctagtttgctattttgacactctctgtttctccctattcccagccttctctctgataactcctgtggtatcaacgtaggatagctttgttttcct
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GCCCTGTTATGACCAAATTCACTATTGCATTGAGAGAGATTGGGACATACAAGGAAGTTCTTCGCTCCCAGgtaaagataatattttctttctgtttcggtgaaagcttccagttttactgctgtccagtgatcaatgctacttgattttgataaaatgttatcctgcacc-
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S177_40V6.1 (Physcomitrella patens), 5'ss of exon 4
GACCGGTAATGACGAAATTTACAATTGCGTTGAGGGAAATTGGGACTTATAAGGAAGTTCTTCGGTCACAGgtatgctagtttgctattttgacactctctgtttctccctattcccagccttctctctgataactcctgtggtatcaacgtaggatagctt-tgttttcct--
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GTCCTGTGATGACAAAATTCACAATTGCTTTGAGGGAGATAGCGACATATAAGGAAGTCCTCCGTTCACAGgtacacagagatttgggtgcttctccttctgctactcgct--tgcatggtttgtatattttaagtcct-tggtcatttcctacaatgattcctggtctaaagtMapped 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|19877169|gb|AU238000.1|AU238000EST: CAATTGCGTTGAGGGAAATTGGGACTTATAAGGAAGTTCTTCGGTCACAG GTGGAACAT-TACTGAATGACAGATTAC
genomic: CAATTGCGTTGAGGGAAATTGGGACTTATAAGGAAGTTCTTCGGTCACAGgtatgctagt ... ccattgtcagGTGGAACATATACTGAATGACAGATTAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GACCGGTAATGACGAAATTTACAATTGCGTTGAGGGAAATTGGGACTTATAAGGAAGTTCTTCGGTCACAGgtatgctagtttgctattttgacactctctgtttctccctattcccagccttctctctgataactcctgtggtatcaacgtaggatagctttgttttcct
- - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccctat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctctct