Sequence
atgc intronic sequence ATGC exonic sequencegtaacttttcgttgaaaagtattggtttgtgttgttgtaggttttgagtggataagatcgccatctgttgaagcctttatctagtttccttgtacattgttctagagagtaaatttccttcatagcattttggatgccttagttattaacattttgttaacatttttcttatggtttgctagATGGCAGAGCAGTTCAACCAGGAACTATCTTTGGCTGGGAAAATCCCGTCAGGTCTCTTCAATGCCATGTTTGAATTCTCGAGCTGTTGGCAGAAAGACG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G24290.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G24290.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g07194.2 (Oryza sativa), 3'ss of exon 2
gtaacttttcgttgaaaagtattggtttgtgttgttgtaggttttgagtggataagatcgccatctgttgaagcctttatctagtttccttgtacattgttctagagagtaaatttcctt-catagcattttggatgccttagttattaacattt-tgttaacatttttcttatg-gtttgctagATGGCAGAGCAGTTCAACCAGGAACTATCTTTGGCTGGGAAAATCCCGTCAGGTCTCTTCAATGCCATGTTTGAATTCTCGAGCTGTTGGCAGAAAGACG
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-------------------------------------------------------------------------------------ttcctcttcagctgtcatggaagccgctttaagtcgcagagtataattacatctataaaaggtaatatttgtgttcctgaagttgtgaagcattttgcagATGTCGGAGCAATTCAACCAGGAATTATCTTTGTCTGGGAAAATTCCATCTGGTTTATTCAATACTATGTTTGAATTTACTGGCTGCTGGCAGAAAGATG
upper sequence: AT4G24290.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G00440.1 (Glycine max), 3'ss of exon 1
gtaacttttcgttgaaaagtattggtttgtgttgttgtaggttttgagtggataagatcgccatctgttgaagcctttatctagtttcct--tgtacattgttctagagagtaaatttccttcatagcattttggatgccttagttattaacattttgttaacatttttcttatggtttgctagATGGCAGAGCAGTTCAACCAGGAACTATCTTTGGCTGGGAAAATCCCGTCAGGTCTCTTCAATGCCATGTTTGAATTCTCGAGCTGTTGGCAGAAAGACG
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-----------------------------------------------------------------------agtggtaatgaattttctttttgtcaacagttttaagtattaagtaatgcatgcatcatctc-----cctt--tcactgactgtttgct----ccttttaaatgtttt--cagATGTCAGAGCAATTCAATCAGGAGTTATCTTTGACTGGCAAGATTCCCTCAGGTCTTTTCAATACAATGTTTGAATTTTCTGGGAGTTGGCAAAGAGATG
upper sequence: AT4G24290.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G28780.1 (Glycine max), 3'ss of exon 2
gtaacttttcgttgaaaagtattggtttgtgttgttgtaggttttgagtggataagatcgccatctgttgaagcctttatctagtttcct--tgtacattgttctagagagtaaatttccttcatagcattttggatgccttagttattaacattttgttaacatttttcttatggtttgctagATGGCAGAGCAGTTCAACCAGGAACTATCTTTGGCTGGGAAAATCCCGTCAGGTCTCTTCAATGCCATGTTTGAATTCTCGAGCTGTTGGCAGAAAGACG
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-----------------------------------------------------------------------agtggtaatgaattttctttttgtcaactgttttaagtattaagtaatgcatgcatcgtctc-----cctt--tcattcactgtttgct----ccttttaaatgtttt--cagATGTCAGAGCAATTCAATCAGGAGTTATCTTTGACTGGCAAGATTCCCTCAGGTCTTTTCAATACAATGTTTGAATTTTCTGGGAGTTGGCAAAGAGATG
upper sequence: AT4G24290.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0035g01040.t01 (Vitis vinifera), 3'ss of exon 2
gtaacttttcgttgaaaagtattggtttgtgttgttgtaggttttgagtggataagatcgccatctgttgaagcctttatctagtttccttgtacattgttctagagagtaaatttccttcatagcattttggatgccttagttattaacattttgt-taacatttttcttatggtttgct--agATGGCAGAGCAGTTCAACCAGGAACTATCTTTGGCTGGGAAAATCCCGTCAGGTCTCTTCAATGCCATGTTTGAATTCTCGAGCTGTTGGCAGAAAGACG
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------------------------------------------------------------------------------------ttgttttacagttaattctag-gacaatgttgatgctgtagcatattaaattcctctttcattgatttcgggtgcattgatatttctttactttgctccagATGTCAGAGCAATTCAACCAGGAGATATCCTTGACTGGTAAAATTCCATCAGGCCTCTTCAATGCTATGTTTGAATTTTCAGGCTGTTGGCAGAAAGATGMapped 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|47829235|gb|CK118919.1|CK118919EST: ATAAAGGGGAGCGTATGCGGTTTAGGTCCGATATTCTTCCTTTCCAACAG ATGGCAGAGCAGTTCAACCAGGAACTATCTTTGGCTGGTAAAATCCCGTCA
genomic: ATAAAGGGGAGCGTATGCGGTTTAGGTCCGATATTCTTCCTTTCCAACAGgtaacttttc ... ggtttgctagATGGCAGAGCAGTTCAACCAGGAACTATCTTTGGCTGGGAAAATCCCGTCA
EST:
gi|116428850|gb|EG471442.1|EG471442EST: ATAAAGGGGAGCGTATGCGGTTTAGGTCCGATATTCTTCCTTTCCAACAG ATGGCAGAGCAGTTCAACCAGGAACTATCTTTGGCTGGGAAAATCCCGTCA
genomic: ATAAAGGGGAGCGTATGCGGTTTAGGTCCGATATTCTTCCTTTCCAACAGgtaacttttc ... ggtttgctagATGGCAGAGCAGTTCAACCAGGAACTATCTTTGGCTGGGAAAATCCCGTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttggatgccttagttattaacattttgttaacatttttcttatggtttgctagATGGCAGAGCAGTTCAACCAGGAACTATCTTTGGCTGGGAAAATCCCGTCAGGTCTCTTCAATGCCATGTTTGAATTCTCGAGCTGTTGGCAGAAAGACG
ttagttattaacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacttttcgttgaaaagtattggtttgtgttgttgtaggttttgagtggataagatcgccatctgttgaagcctttatctagtttccttgtacattgttctagagagtaaatttccttcatagcattttggatgccttagttattaacattttgttaacatttttcttatggtttgctagATGGCAGAGCAGTTCAACCAGGAACTATCTTTGGCTGGGAAAATCCCGTCAGGTCTCTTCAATGCCATGTTTGAATTCTCGAGCTGTTGGCAGAAAGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT