Sequence
atgc intronic sequence ATGC exonic sequencegtatactgacgttccttcactaacaacaaaattgggttgatcttggtacttagtttgaaacaaatagtgacaccttgtttggcactaaaatggatatatctaaagaaaccatgggtatctggtctttcgtttcagctatccccacatctagttgtatgatattcttactcatcatttcatttcagTGTAAAAGAGAAGGCTTTGTGCAAAAGGTAAAAGATGAAGAAGGTGAAGGTTGTAATGTTCACGGTTTCTTGGAAGTTAACAAAGTTGCTGGGAACTTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G22200.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G22200.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G24610.1 (Glycine max), 3'ss of exon 6
gtatactgacgttccttcactaacaacaaaattgggttgatcttggtacttagtttgaaacaaatagtgacaccttgtttggcactaaaatggatatatctaaagaaaccatgggtatctggtctttcgtttcagctatccccacatctagttgtatgatattcttactcatca--tttcatttcagTGTAAAAGAGAAGGCTTTGTGCAAAAGGTAAAAGATGAAGAAGGTGAAGGTTGTAATGTTCACGGTTTCTTGGAAGTTAACAAAGTTGCTGGGAACTTTC
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---------------------------------------------------------------------------------taattatattggacttgtgtactttgccct--gatgtttgaatttgtagtgggaattttgtcaga----gaaatattgcattctgacgctttggtttttctttcagTGTCAAAGAGAGGGTTATGTGCAAAGGGTAAAGGATGAAGAAGGTGAAGGATGCAATCTTCAAGGATCTCTTGAAGTTAATAAAGTAGCAGGAAATTTTC
upper sequence: AT1G22200.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G07840.1 (Glycine max), 3'ss of exon 6
gtatactgacgttccttcactaacaacaaaattgggttgatcttggtacttagtttgaaacaaatagtgacaccttgtttggcactaaaatggatatatctaaagaaaccatgggtatctggtctttcgtttcagctatccccacatctagttgtatgatattcttactcatca--tttcatttcagTGTAAAAGAGAAGGCTTTGTGCAAAAGGTAAAAGATGAAGAAGGTGAAGGTTGTAATGTTCACGGTTTCTTGGAAGTTAACAAAGTTGCTGGGAACTTTC
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------------------------------------------------------------------------------tta--attatattggatttgtgtactttgccct--gatgttgaatttgtagtgggaattttgtagg-----aggtatattgcattctgacactttggttttgcttttagTGTCAAAGAGAGGGTTATGTGCAAAGGGTAAAGGATGAAGAAGGTGAAGGATGCAATCTTCAAGGATCTCTTGAAGTTAATAAAGTAGCAGGAAATTTTC
upper sequence: AT1G22200.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv12s0178g00020.t01 (Vitis vinifera), 3'ss of exon 6
gtatactgacgttccttcactaacaacaaaattgggttgatcttggtacttagtttgaaacaaatagtgacaccttgtttggcactaaaatggatatatctaaagaaaccatgggtatctggtctttcgtttcagctatccccacatctagttgtatgatattcttactcatcatttcatttcagTGTAAAAGAGAAGGCTTTGTGCAAAAGGTAAAAGATGAAGAAGGTGAAGGTTGTAATGTTCACGGTTTCTTGGAAGTTAACAAAGTTGCTGGGAACTTTC
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-----------------------------------------------------------------------tctttttgaatctttctagctcttaggcttgtgaaaatgataaacattttctattgttatatagtt-tttgagcttataattatatgtt------------tgttgcattt-agTGCAAAAGAGAAGGCTTTGTCCAAAAGGTTAAAGAGGAAGAAGGTGAAGGATGCAATGTCTATGGCTTTTTAGAAGTTAATAAAGTTGCAGGAAACTTTCMapped 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|164225769|gb|EL973674.1|EL973674EST: CCGAAAGAAAGGTTGGGCCCTCTCGGACCCTGAATCAATCGACCAG TGTAAAAGAGAAGGCTTTGTGCAAAAGGTAAAAGATGAAGAAGGTGAAGGT
genomic: CCGAAAGAAAGGTTGGGCCCTCTCGGACCCTGAATCAATCGACCAGgtatactgac ... ttcatttcagTGTAAAAGAGAAGGCTTTGTGCAAAAGGTAAAAGATGAAGAAGGTGAAGGT
EST:
gi|124781711|gb|EH871654.1|EH871654EST: CTTACCGAAAGAAAGGTTGGGCCCTCTCGGACCCTGAATCAATCGACCAG TGTAAAAGAGAAGGCTTTGTGCAAAAGGTAAAAGATGAAGAAGGTGAAGGT
genomic: CTTACCGAAAGAAAGGTTGGGCCCTCTCGGACCCTGAATCAATCGACCAGgtatactgac ... ttcatttcagTGTAAAAGAGAAGGCTTTGTGCAAAAGGTAAAAGATGAAGAAGGTGAAGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcagctatccccacatctagttgtatgatattcttactcatcatttcatttcagTGTAAAAGAGAAGGCTTTGTGCAAAAGGTAAAAGATGAAGAAGGTGAAGGTTGTAATGTTCACGGTTTCTTGGAAGTTAACAAAGTTGCTGGGAACTTTC
ttcttac putative branch site (score: 2)
tttcatttc putative PPT
tatgatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatactgacgttccttcactaacaacaaaattgggttgatcttggtacttagtttgaaacaaatagtgacaccttgtttggcactaaaatggatatatctaaagaaaccatgggtatctggtctttcgtttcagctatccccacatctagttgtatgatattcttactcatcatttcatttcagTGTAAAAGAGAAGGCTTTGTGCAAAAGGTAAAAGATGAAGAAGGTGAAGGTTGTAATGTTCACGGTTTCTTGGAAGTTAACAAAGTTGCTGGGAACTTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG