Sequence
atgc intronic sequence ATGC exonic sequencegtaaattctttcggattcgttggcaatgtttccctgtattgattatggttttatactcttttgaggtgcatagttatgaacttttcatgttttcttcactctagGGTCAAAAATTGATGATGATGGGAACTGCAGATGAAATAGTGAAGGCTCCAGAGAAGGGTCCTGTTTTTATGGAGGATCTTCCTGAAGAACAGCAGGCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21280.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 3
---------gtaaattctttcggattcgt-tggcaatgtttccctgtattgattatggttttatactcttttg-aggtgcatagttatgaacttttcatgttttcttcactctagGGTCAAAAATTGATGATGATGGGAACTGCAGATGAAATAGTGAAGGCTCCAGAGAAGGGTCCTGTTTTTATGGAGGATCTTCCTGAAGAACAGCAGGCTG
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gtgagattatcaacctgtcttccattcacatttttattctaccagacccttaatacattcaagtattcaactacatgtatataatgttaaggattggaaatgcactctgc---agGGTCAAAAATTGATGATGATAGGTACAGCTGATGAGATTGTGAAAGCTCCAGAGAAAGGACCAGTATTTGTAGAGGATCTACCAGAAGAAGAGCAAGTGG
upper sequence: AT3G21280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G017086_T01 (Zea mays), 3'ss of exon 3
----gtaaattctttcggattcgttggcaatgtttccctgtattgattatggttttatactcttttgaggtgcatagttatgaacttttcatgttttcttcactctagGGTCAAAAATTGATGATGATGGGAACTGCAGATGAAATAGTGAAGGCTCCAGAGAAGGGTCCTGTTTTTATGGAGGATCTTCCTGAAGAACAGCAGGCTG
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gtgagatgcttggcttattttctgtgctcatattttgttgtatcaa--gtgctcaaatgctgtattaagttgcctcaaatagaactgaatttgaaatgcgctctgcagGGCCAAAAGTTGATGATGATAGGCACGGCTGATGAGATTGTGAAAGCTCCGGAGAAAGGTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGA
upper sequence: AT3G21280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 3
gtaaattctttcggattcgttggcaatgtttccctgtattgattatggttttatactcttttgaggtgcatagttatgaacttttcatgttttcttcactctagGGTCAAAAATTGATGATGATGGGAACTGCAGATGAAATAGTGAAGGCTCCAGAGAAGGGTCCTGTTTTTATGGAGGATCTTCCTGAAGAACAGCAGGCTG
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--------gttgagcggtgctag-aatgtgttttt-catt-accattcgactatattccatatgccttttcatttaattgatctacataatcttctt-ttccagGGTCAAAAGCTAATGATGATGGGTACAGCTGATGAAGTTGTGAAGACTCCTGAGAAGGGAACTGTTTTTGTTGAAGATCTTCCAGAAGAAGAACAAGTAG
upper sequence: AT3G21280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G01480.1 (Glycine max), 3'ss of exon 3
gtaaattctttcggattcgttggcaatgtttccctgtattgattatggttttatactcttttgaggtgcatagttatgaacttttcatgttttcttcactctagGGTCAAAAATTGATGATGATGGGAACTGCAGATGAAATAGTGAAGGCTCCAGAGAAGGGTCCTGTTTTTATGGAGGATCTTCCTGAAGAACAGCAGGCTG
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--------gttaggatgc-tagaatgtgcttttcgttaccgttcaa----ctatattccgtacatcttttcatttaatagatctacataatcttctttttccagGGTCAAAAGCTAATGATGATGGGTACAGCTGATGAAGTTGTAAAGACTCCTGAGAAGGGAACTGTTTTTGTTGAAGATCTTCCTGAAGAAGAACAAGTAG
upper sequence: AT3G21280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 3
gtaaattctttcggattcgttggcaatgtttccctgtattgattatggttttatactcttttgaggtgcatagttatgaacttttcatgttttcttcactctagGGTCAAAAATTGATGATGATGGGAACTGCAGATGAAATAGTGAAGGCTCCAGAGAAGGGTCCTGTTTTTATGGAGGATCTTCCTGAAGAACAGCAGGCTG
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gtgaatgatctacggcttatt-----tgcttctct-tttttcctgtgcttgtagaatttgttgttcaata-agatgtacaatattcatttttttc-------agGGTCAAAAATTGATGATGATGGGAACTGCAGATGAGATTGTTAAGGCCCCGGAGAAGGGCCCTGTTTTCATGGAGGATCTTCCTGAAGAAGAGCAAGTGGMapped 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|19876163|gb|AU236994.1|AU236994EST: GATGATGCAGATTGGTCTACGTTGGGACTGAAAAAT GGTCAAAAATTGATGATGATGGGAACTGCAGATGAAATAGTGAAGGCTCCA
genomic: GATGATGCAGATTGGTCTACGTTGGGACTGAAAAATgtaaattctt ... ttcactctagGGTCAAAAATTGATGATGATGGGAACTGCAGATGAAATAGTGAAGGCTCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatactcttttgaggtgcatagttatgaacttttcatgttttcttcactctagGGTCAAAAATTGATGATGATGGGAACTGCAGATGAAATAGTGAAGGCTCCAGAGAAGGGTCCTGTTTTTATGGAGGATCTTCCTGAAGAACAGCAGGCTG
cttttcatgttttctt CT-rich tract
atagttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattctttcggattcgttggcaatgtttccctgtattgattatggttttatactcttttgaggtgcatagttatgaacttttcatgttttcttcactctagGGTCAAAAATTGATGATGATGGGAACTGCAGATGAAATAGTGAAGGCTCCAGAGAAGGGTCCTGTTTTTATGGAGGATCTTCCTGAAGAACAGCAGGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC