Sequence
atgc intronic sequence ATGC exonic sequence...gaatcgttactatacaagagtagtttgtaaggcgtcaaactagcctatcattacatttggtttggtatactcacaagtttttttttttttgtttctatagGACTAAACTACGACGAGCAAATGTAAATTTTCTTTCTGCTCCAATCAAGGACGGAACAACAGGAACAGTGATAGTTCTCACAACTCCTGATGCACAACGT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G27600.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G27600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G01920.1 (Glycine max), 3'ss of exon 2
gaatcgttactatacaagagta--gtttgtaaggcgtcaaactagcctatcattacatttggtttggtatactcacaagtttttttttttttgtttcta--tagGACTAAACTACGACGAGCAAATGTAAATTTTCTTTCTGCTCCAATCAAGGACGGAACAACAGGAACAGTGATAGTTCTCACAACTCCTGATGCACAACGT
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---tctatgttatttaataattccatcaattttgttttgggcaagtgaggtttgatgaatacttatat-tgcttgtttgtattatttttttaaaaaaaaattagGGAAAAATTACGCCGAGCAAATGTGCAATTTCTTTCTGCACCAATCAAGGATGGGACTACTGGAACAGTTATAGTTCTCACAACTCCAGATGCCCAGCGC
upper sequence: AT4G27600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G11620.1 (Glycine max), 3'ss of exon 2
----gaatcgttactatacaa--gagtagtttgtaaggcgtcaaactagcctatcattacatttggtttggtatactcacaagtttttttttttttgtttctatagGACTAAACTACGACGAGCAAATGTAAATTTTCTTTCTGCTCCAATCAAGGACGGAACAACAGGAACAGTGATAGTTCTCACAACTCCTGATGCACAACGT
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tggacacaggtttctatgttatttaatgattccatcagttttgttttgggcaa--gtgagatttgatcaggtttgtttaca----tttgatttttactttttttagGGAGAAATTACGCCGAGCAAATGTGCAATTTCTTTCTGCACCAATGAAGGATGGGACAACTGGAACAGTTATAGTCCTCACAACTCCAGATGCCCAGCGC
upper sequence: AT4G27600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0039g01580.t01 (Vitis vinifera), 3'ss of exon 2
gaatcgttactatacaagagtagtttgtaaggcgtcaaactagcctatcattacatttggtttggtatactcacaagtttttttttttttgtt-tctatagGACTAAACTACGACGAGCAAATGTAAATTTTCTTTCTGCTCCAATCAAGGACGGAACAACAGGAACAGTGATAGTTCTCACAACTCCTGATGCACAACGT
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gagatac-attcaattatgatgtctcggttgctgataagaagaagtgtggctccaatgatcttctttaactaactacatactgtcttgatatggtttgtagAACAAAATTGCGTCGGGCAAATGTGAATTTTCTCTCTGCACCTGTTAAGGATGGGACAACGGGGACAGTGATAGTTCTCACGACTCCAGATGCTCAGCGCMapped 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|124765711|gb|EH855841.1|EH855841EST: TGGCAATGGCTGGCAGTATTGGAGGTGACCCTACTCGGTAGCTTTTACGG GACTAAACTACGACGAGCA
genomic: TGGCAATGGCTGGCAGTATTGGAGGTGACCCT-CTCGGTAGCTTTTACGGgtactaaact ... gtttctatagGACTAAACTACGACGAGCA
EST:
gi|164116023|gb|ES047400.1|ES047400EST: GTGGCAATGGCTGGCAGTATTGGAGGTGACCCTCTCGGTAGCTTTTACGG GACTAAACTACGACGAGCAAATGTAAA
genomic: GTGGCAATGGCTGGCAGTATTGGAGGTGACCCTCTCGGTAGCTTTTACGGgtactaaact ... gtttctatagGACTAAACTACGACGAGCAAATGTAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcattacatttggtttggtatactcacaagtttttttttttttgtttctatagGACTAAACTACGACGAGCAAATGTAAATTTTCTTTCTGCTCCAATCAAGGACGGAACAACAGGAACAGTGATAGTTCTCACAACTCCTGATGCACAACGT
tactcac putative branch site (score: 1)
tttttttttttttgtt putative PPT
acaagttttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaatcgttactatacaagagtagtttgtaaggcgtcaaactagcctatcattacatttggtttggtatactcacaagtttttttttttttgtttctatagGACTAAACTACGACGAGCAAATGTAAATTTTCTTTCTGCTCCAATCAAGGACGGAACAACAGGAACAGTGATAGTTCTCACAACTCCTGATGCACAACGT
- - - - - -atacaag
- - - - - - - - - - -agtttgt
- - - - - - - - - - - - - - - - - -caaacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actcaca