Sequence
atgc intronic sequence ATGC exonic sequencegttttgtttcctctgatttgaaattgtgatctatgtgtttgggatctgtttagggttttgatgcagagtttgttatttggttcactattgaattaagattgggttttgatgttgaaacgtttttagGATGAAAAGTATTGGTCTTTGCTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G42950.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G17170.1 (Glycine max), 3'ss of exon 1
gttttgtttcctctgatttgaaattgtgatctatgtgtttgggatctgtttagggttttgatgcagagtttgttatttggttcactattgaattaagattgggttttgatgttgaaacgtttttagGATGAAAAGTATTGGTCTTTGCTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATC
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------ttctctttgatctatttctttcat-tacat-------atctcttccactctctcat----aagtaaacattttactgac------actatatttgtcatcttacgt--gatggctaacagGATGAAAAATATTGGCCATTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G05550.1 (Glycine max), 3'ss of exon 1
gttttgtttcctctgatttgaaattgtgatctatgtgtttgggatctgtttagggttttgatgcagagtttgttatttggttcactattgaattaagattgggttttgatgttgaaacgtttttagGATGAAAAGTATTGGTCTTTGCTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATC
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----------ctttgat----aaatctatttctttcattacatatctcttccgctctctcat----aattaaacattttactgac------actatatttgtcatcttacgt--gatggctaacagGATGAAAAATATTGGCCACTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G08270.1 (Glycine max), 3'ss of exon 1
gttttgtttcctctgatttgaaattgtgatctatgtgtttgggatctgtttagggttttgatgcagagtttgttatttggttcactattgaattaagattgggttttgatgttgaaacgtttttagGATGAAAAGTATTGGTCTTTGCTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATC
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----------------------ctcgaactctatctattttgc-tttacatgtctctttccctcactcttgattaaaacattt--tacttactttatgtttg-ttatcctgtgtgatgattaacagGATGAAAAGTATTGGCCATTGATGCCCGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCTGGTCCTCGATATAGCAGTTTAATTCATGGTCAAAATC
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G19820.1 (Glycine max), 3'ss of exon 1
gttttgtttcctctgatttgaaattgtgatctatgtgtttgggatctgtttagggttttgatgcagagtttgttatttggttcactattgaattaagattgggttttgatgttgaaacgtttttagGATGAAAAGTATTGGTCTTTGCTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATC
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-------------------------atattttttgc-tttacatctaacctaatgtctctttccacatctcttgattaaaacattttacttactatatatttgttatcctgtgtgatgattaacagGATGAAAAGTATTGGCCACTGATGCCTGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCCGGTCCTCGATATAGTAGTTTAATTCATGGTCAAAATC
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv11s0016g00720.t01 (Vitis vinifera), 3'ss of exon 1
gttttgtttcctctgatttgaaattgtgatctatgtgtttgggatctgtttagggttttgatgcagagtttgttatttggttcactattgaattaagattgggttttgatgttgaaacgtttttagGATGAAAAGTATTGGTCTTTGCTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATC
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--------------gatattcaat---aaactatcatattatgactagtgttagcatttatcgtataagc-gaagtttggcttatt-ttggttctttcttcttatgtgacatttaa-------cagGATGAGAAGTATTGGCCACTGATGCCTCCCTTGCCTTCATATGGGTATGGGAGAGAGCATCGTGGAGCTCGATATGGGAGTTTGATTCATGGTCAAAATCMapped 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|164095637|gb|ES123391.1|ES123391EST: AGATTCTTGCTCTTCAG GATGAAAAGTATTGGTCTTTGCTTCCTCCTTTACCTTCATATGGATATGGA
genomic: AGATTCTTGCTCTTCAGgttttgtttc ... acgtttttagGATGAAAAGTATTGGTCTTTGCTTCCTCCTTTACCTTCATATGGATATGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttatttggttcactattgaattaagattgggttttgatgttgaaacgtttttagGATGAAAAGTATTGGTCTTTGCTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATC
ttttgat putative branch site (score: 4)
cgttttt putative PPT
tattgaattaagatt 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
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gttttgtttcctctgatttgaaattgtgatctatgtgtttgggatctgtttagggttttgatgcagagtttgttatttggttcactattgaattaagattgggttttgatgttgaaacgtttttagGATGAAAAGTATTGGTCTTTGCTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATC
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