Sequence
atgc intronic sequence ATGC exonic sequence...aagcacagcttgtattatgatctcattgttctatgttttgcatacatgtaaggtcataaaaaaatgttatctatactaacaccaattcaacaaacttaagGTTGTGTATGTTGGAGATGGGAACAACATGGTTCACTCTTGGTTAGAATTGGCATCCGTTATTCCATTCCACTTTGTCTGCGCTTGCCCAAAAGGGTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G75330.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G75330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G349547_T01 (Zea mays), 3'ss of exon 3
aagcacagcttgtattatgat-ctcattgttctatgttttgcatacatgtaaggtcataaaaaaatgttatctatactaacaccaattcaacaaacttaagGTTGTGTATGTTGGAGATGGGAACAACATGGTTCACTCTTGGTTAGAATTGGCATCCGTTATTCCATTCCACTTTGTCTGCGCTTGCCCAAAAGGGTATG
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--------gtagaatcataacactgaattatctgcgtttgacctgtgtctaattttgagtttttgggttgtaaccaattgtcttcttcgattgcgttgtagGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTGGCTGATGTGCTTCCTTTTCACTTTGTATGTGCTTGTCCCAAGGGATTTG
upper sequence: AT1G75330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G050371_T01 (Zea mays), 3'ss of exon 3
aagcacagcttgtattatgat-ctcattgttctatgttttgcatacatgtaaggtcataaaaaaatgttatctatactaacaccaattcaacaaacttaagGTTGTGTATGTTGGAGATGGGAACAACATGGTTCACTCTTGGTTAGAATTGGCATCCGTTATTCCATTCCACTTTGTCTGCGCTTGCCCAAAAGGGTATG
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--------gtagaatcataacactgaattaactgtgtttggcctgtgtctaattttgagtttctgggttgtaaccaattgtcttcttcgattgcgttgtagGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTGGCTGCTGTGCTTCCTTTTCACTTTGTATGTGCTTGTCCCAAGGGATTTG
upper sequence: AT1G75330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G157210_T01 (Zea mays), 3'ss of exon 6
aagcacagcttgtattatgat-ctcattgttctatgttttgcatacatgtaaggtcataaaaaaatgttatctatactaacaccaattcaacaaacttaagGTTGTGTATGTTGGAGATGGGAACAACATGGTTCACTCTTGGTTAGAATTGGCATCCGTTATTCCATTCCACTTTGTCTGCGCTTGCCCAAAAGGGTATG
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--------gtagaatcataacactgaattatctgcgtttgacctgtgtctaattttgagtttctgggttgtaaccaattgtcttcttcgattgcgttgtagGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGTTATTGGCTGATGTGCTTCCTTTTCACTTTGTATGTGCTTGTCCCAAGGGATTTG
upper sequence: AT1G75330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G046748_T02 (Zea mays), 3'ss of exon 4
aagcacagcttgtattatgatctcattg-ttctatgttttgcatacatgtaaggtcataaaaaaatgttatctatactaacaccaattcaacaaacttaagGTTGTGTATGTTGGAGATGGGAACAACATGGTTCACTCTTGGTTAGAATTGGCATCCGTTATTCCATTCCACTTTGTCTGCGCTTGCCCAAAAGGGTATG
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----gtagatcatcgtatcactgaagtaactgcatgtgctctatgcgtctaatttcg-agatgggttctgacca-actgccttc--ttcaattgtgt--agGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCGTGGCTTCTATTGGCTGCTGTACTTCCTTTTCACTTTGTATGTGCTTGTCCCAAGGGATTTG
upper sequence: AT1G75330.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G062142_T01 (Zea mays), 3'ss of exon 5
aagcacagcttgtattatgat-ctcattgttctatgttttgcatacatgtaaggtcataaaaaaatgttatctatactaacaccaattcaacaaacttaagGTTGTGTATGTTGGAGATGGGAACAACATGGTTCACTCTTGGTTAGAATTGGCATCCGTTATTCCATTCCACTTTGTCTGCGCTTGCCCAAAAGGGTATG
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--------gtagaatcataacactgaattatccgcgtttgacctgtgtctatttttgagtttctgggttgtaaccaattgtcttcttcgattacgttgtagGTTGTCTATGTTGGAGATGGGAACAACATTGTGCACTCATGGCTGCTATTGGCTGTTGTGCTTCCTTTTCACTTTGTATGTGCTTGTCCCAAGGGATTTGMapped 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|86080147|gb|DR375904.1|DR375904EST: GTCAAGTTGAAGGGACAAAG GTTGTGTATGTTGGAGATGGGAACAACATGGTTCACTCTTGGTTAGAATTG
genomic: GTCAAGTTGAAGGGACAAAGgttagttaac ... caaacttaagGTTGTGTATGTTGGAGATGGGAACAACATGGTTCACTCTTGGTTAGAATTG
EST:
gi|125212385|gb|EL227339.1|EL227339EST: CCGATGCCCTCACAATGATAGAGCACATTGGTCAAGTTGAAGGGACAAAG GTTGTGTATGTTGGAGATGGGAACAACATGGTTCACTCTTGGTTAGAATTG
genomic: CCGATGCCCTCACAATGATAGAGCACATTGGTCAAGTTGAAGGGACAAAGgttagttaac ... caaacttaagGTTGTGTATGTTGGAGATGGGAACAACATGGTTCACTCTTGGTTAGAATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtaaggtcataaaaaaatgttatctatactaacaccaattcaacaaacttaagGTTGTGTATGTTGGAGATGGGAACAACATGGTTCACTCTTGGTTAGAATTGGCATCCGTTATTCCATTCCACTTTGTCTGCGCTTGCCCAAAAGGGTATG
tactaac putative branch site (score: 0)
ataaaaaaatgttatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagcacagcttgtattatgatctcattgttctatgttttgcatacatgtaaggtcataaaaaaatgttatctatactaacaccaattcaacaaacttaagGTTGTGTATGTTGGAGATGGGAACAACATGGTTCACTCTTGGTTAGAATTGGCATCCGTTATTCCATTCCACTTTGTCTGCGCTTGCCCAAAAGGGTATG
aagcaca
- - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - catacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaccaa