Sequence
atgc intronic sequence ATGC exonic sequencegtttcttcttaaccctagaatttttaggttttacttaattgtatttaatacccttttgatctgatctattgatctgatgttgctgatttggaatttggtttcagctttatagattggtgataaagttttgatttttttttgttgttgttgcagAAACTGGATTTTAAGTTTCCACTATCGGTTTCATGTGTTCACTTCATATGTTCGTCGATTGGAGCTTACATCGTTATCAAAGTTCTCAAGCTTAAACCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G77610.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G77610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os08g01410.1 (Oryza sativa), 3'ss of exon 1
gtttcttcttaaccctagaatttttaggttttacttaattgtatttaatacccttttgatctgatctattgatctgatgttgctgatttggaatttggtttcagctttatagattggtgataaagttttgatttttttttgttgttgttgcagAAACTGGATTTTAAGTTTCCACTATCGGTTTCATGTGTTCACTTCATATGTTCGTCGATTGGAGCTTACATCGTTATCAAAGTTCTCAAGCTTAAACCAT
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--------------------------------------------ttgggagtccaaaattgtgttcttttt-cagaatattactgcataatcattca--cacaagtcatcaatttgatg-----gttttcatttttttttcct-tggatgcagAAATTGGAGTTCAAGTTCCCTCTTACTGTCTCGTGTGTCCACTTTATATGCTCTTCGATTGGAGCTTACATCGCAATCAAAATTCTCAAGATGAAACCAC
upper sequence: AT1G77610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G11850.1 (Glycine max), 3'ss of exon 1
gtttcttcttaaccctagaatttttaggttttacttaattgtatttaatacccttttgatctgatctattgatctgatgttgctgatttggaatttggtttcagctt-tatagattggtgataaagttttgatttttttttgttgttgttgcagAAACTGGATTTTAAGTTTCCACTATCGGTTTCATGTGTTCACTTCATATGTTCGTCGATTGGAGCTTACATCGTTATCAAAGTTCTCAAGCTTAAACCAT
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-----------------------------------------------attcattcttactcacctttgttactcaa---tcatcaattcatcatat--tataaacttgtatggattatatagcaaacactaacatttttttttt--tgttacagAAATTGGATTTCAAGTTTCCCCTATCAGTTTCCTGTGTCCACTTTATCTGTTCATCCATTGGAGCTTATGTGGTAATTAAGTTGCTGAAGCTTAAACCAC
upper sequence: AT1G77610.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0001g02970.t01 (Vitis vinifera), 3'ss of exon 1
gtttcttcttaaccctagaatttttaggttttacttaattgtatttaatacccttttgatctgatctattgatctgat-gttgctgatttggaatttggtttcagctttatagattggtgataaagttttgatttttttttgttgttgttgcagAAACTGGATTTTAAGTTTCCACTATCGGTTTCATGTGTTCACTTCATATGTTCGTCGATTGGAGCTTACATCGTTATCAAAGTTCTCAAGCTTAAACCAT
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---------------------------------------tggaaaaaggaattgtttggtccctttcatttgtttcattgttcatgact----gcatggttatgatct---gaatttctgg-gaatctgaagtaatttcttgt-------gcagAAACTGGATTTCAAATTTCCTCTGTCAGTGTCATGTATTCACTTCATATGCTCTGCTATTGGAGCCTATCTAGTAATCAAGGTACTGAAGCTTAAGCCACMapped 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|164165152|gb|ES049875.1|ES049875EST: AAATGGATCTTTCAG AAACTGGATTTTAAGTTTCCACTATCGGTTTCATGTGTTCACTTCATATGT
genomic: AAATGGATCTTTCAGgtttcttctt ... gttgttgcagAAACTGGATTTTAAGTTTCCACTATCGGTTTCATGTGTTCACTTCATATGT
EST:
gi|163985698|gb|EL971466.1|EL971466EST: GTTACCGTCATCATCATGAACAAATGGATCTTTCAG AAACTGGATTTTAAGT
genomic: GTTACCGTCATCATCATGAACAAATGGATCTTTCAGgtttcttctt ... gttgttgcagAAACTGGATTTTAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcagctttatagattggtgataaagttttgatttttttttgttgttgttgcagAAACTGGATTTTAAGTTTCCACTATCGGTTTCATGTGTTCACTTCATATGTTCGTCGATTGGAGCTTACATCGTTATCAAAGTTCTCAAGCTTAAACCAT
ttttgat putative branch site (score: 4)
tttttttttgttgtt CT-rich tract
ataaagttttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttcttcttaaccctagaatttttaggttttacttaattgtatttaatacccttttgatctgatctattgatctgatgttgctgatttggaatttggtttcagctttatagattggtgataaagttttgatttttttttgttgttgttgcagAAACTGGATTTTAAGTTTCCACTATCGGTTTCATGTGTTCACTTCATATGTTCGTCGATTGGAGCTTACATCGTTATCAAAGTTCTCAAGCTTAAACCAT
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