Sequence
atgc intronic sequence ATGC exonic sequence...tttctgtggccggtatctgaacattaggatgcttatgggctatgtacactcttatccctctctcgaattatagaattcactttcttatgatatgtttcagGCATCTAGTCCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03457.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 2
---tttctgtggccggtatctgaacattaggatgcttatgggctatgtacactcttatccctctctcgaattatagaattcactttcttatgatatgtttcagGCATCTAGTCCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTAG
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ttgggagtaaagcctgttgttgtgatttcagttctgtaaaaccgacat-tacttctattgcgacctcct-tgacagcaattcctttttttctctgaaac-cagGCTTCAAGTCCATTGCAAGTGAAATATGCTGATGGAGAGTTGGAAAGACTGG
upper sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G02700.3 (Glycine max), 3'ss of exon 1
tttctgtggccggtatctgaacattaggatgcttatgggctatgtacactcttatccctctctcgaattatagaattcactttcttatgatatgtttcagGCATCTAGTCCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTAG
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caattgctgacattattgacatctttgcataataactatggtgagatggtattactattctcctgattgggaagcatcttattttttgtgtccaattcagGCATCTAGTCCGTTGCAAGTGAAGTATGCAGATGGTGAATTGGAAAGATTAG
upper sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G17090.1 (Glycine max), 3'ss of exon 2
tttctgtggccggtatctgaacattag---gatgcttatgggctatgtacactcttatccctctctcgaattata-gaattcactttcttatgatatgtttcagGCATCTAGTCCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTAG
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--attgctgacattattgacatctttgcttaataactatggtgtgatgaca-tagtactattctcctgattgggaagcatcctattttttgtg-tccaattcagGCATCTAGTCCGTTACAAGTGAAGTATGCAGATGGCGAATTGGAAAGATTAG
upper sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G39300.1 (Glycine max), 3'ss of exon 2
tttctgtggccggtatctga-acattaggatgcttatgggctatgtacactcttatccctctctcgaattatagaattcactttcttatgatatgtttcagGCATCTAGTCCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTAG
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ttagtaataatgttgtggaagatatttctttagtaacgatgtg-atatgatattattctcattctgatttggaacatcctgtttttctgtgtccatttcagGCATCTAGTCCATTACAAGTGAAGTATGCAGATGGCGAGCTGGAAAGATTAG
upper sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G36650.2 (Glycine max), 3'ss of exon 2
tttctgtggccggtatctgaacattaggatgcttatgggc-tatg-tacactcttatccctctctcgaattatagaattcactttcttatgatatgtttcagGCATCTAGTCCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTAG
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--ttggtaataatgttgaggaagttattgctttagtaaccatgtgatatgatactattctcattctgatttggaacatcctgtttttctgtgtccaattcagGCATCTAGTCCATTACAAGTGAAGTATGCAGATGGGGAGTTGGAAAGATTAG
upper sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0104g01150.t01 (Vitis vinifera), 3'ss of exon 2
tttctgtggccggtatctgaacattagg---atgctta--tgggctatg-tacactcttatccctctct--cgaattatagaattcact-ttcttatgatatgtttcagGCATCTAGTCCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTAG
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---------tcgttgcctaaaaatttgctgcatactttgttaggttgtgatgcattcatgttattctttgtctgattaaaaggtattctgctctttctgtctaattcagGCATCTAGCCCGTTGCAAGTGAAGTATGCAGATGGCGAGTTGGAAAGGCTAGMapped 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|125009159|gb|EL081428.1|EL081428EST: ATGCTGACAAGGTGATCAATAGTTTTCATAACAAGAAGACATTGCCTGGG GCATCCAGTCCGTTGCAAGTTAAGTATGCAGATGGCG
genomic: ATGCTGACAAGGTGATCAATAGTTTTCATAACAAGAAGACATTGCCTGGGgtaagtcttc ... tatgtttcagGCATCTAGTCCGTTGCAAGTTAAGTATGCAGATGGCG
EST:
gi|47830195|gb|CK119879.1|CK119879EST: ATGCTGACAAGGTGATCAATAGTTTTCATAACAAGAAGACATTGCCTGGG GCATCTAGTCCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTA
genomic: ATGCTGACAAGGTGATCAATAGTTTTCATAACAAGAAGACATTGCCTGGGgtaagtcttc ... tatgtttcagGCATCTAGTCCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acactcttatccctctctcgaattatagaattcactttcttatgatatgtttcagGCATCTAGTCCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTAG
aattatagaattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttctgtggccggtatctgaacattaggatgcttatgggctatgtacactcttatccctctctcgaattatagaattcactttcttatgatatgtttcagGCATCTAGTCCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG