Sequence
atgc intronic sequence ATGC exonic sequencegtatttgattattgcttactagacttcttacttatattccacactagttactttgtagactacttacacacgattttccaactgcagGTACGTAGTGGAGAGGATGGATGGTGACCTCTGGGAGAAGGTTCTTACGGAAGAAAATGAATATAGGAGGCAACTTATAGACCAAGTTGTGTCTACTGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11130.1 |
intron # | 23 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 22
gtatttgattattgcttactagacttcttacttatattccacactagttacttt---gtagactacttacacacg-attttccaactgcagGTACGTAGTGGAGAGGATGGATGGTGACCTCTGGGAGAAGGTTCTTACGGAAGAAAATGAATATAGGAGGCAACTTATAGACCAAGTTGTGTCTACTGCT
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------gtttgtggtgtata----tttatatttttttctctaagtaattatccttggattcaatgcttacatgcttatattgggattacagATATGTTGTTGAGAGGATGGATGGTGATCTTTGGGAGAAAGTTCTTAACCCTGATAATGCCTACAGAAGGCAACTTATTGATCAGGTTGTATCTACAGCT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 23
------gtatttgattattgctta-ctagacttcttactt---atattccacactagttactttgtagactacttacacacg---attttccaactgcagGTACGTAGTGGAGAGGATGGATGGTGACCTCTGGGAGAAGGTTCTTACGGAAGAAAATGAATATAGGAGGCAACTTATAGACCAAGTTGTGTCTACTGCT
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ctgcacctccgtcactttagaggagctatatttgtgatccttaatacaccaaatcaattttctttaatacaatgttcacatgcttatattgtgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 23
---gtatttgattattgcttactag----acttcttacttatattccac---actagttactttgtagactacttacacacg---attttccaactgcagGTACGTAGTGGAGAGGATGGATGGTGACCTCTGGGAGAAGGTTCTTACGGAAGAAAATGAATATAGGAGGCAACTTATAGACCAAGTTGTGTCTACTGCT
| | | | | | || | || | || ||||| | | || || | | || | |||| || || | ||| || || || ||||| ||||||||||| | |||| || |||||| || ||||||||||| ||||||||||| || || ||||| |||||||||
agtacactccgtcactttagaggagctctatttgtggtccttaatccaccaaatcaattttctttaattcaacattcacatacttatattttgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 22
gtatttgattattgcttactagacttcttacttatattccacactagttactttgtagactacttacacacg-attttccaactgcagGTACGTAGTGGAGAGGATGGATGGTGACCTCTGGGAGAAGGTTCTTACGGAAGAAAATGAATATAGGAGGCAACTTATAGACCAAGTTGTGTCTACTGCT
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--gtttg--tggtgtatatttatatttttttttct-ctaaatgattatccttggattcaatgcttacatgctcatattgggattacagATATGTTGTTGAGAGGATGGATGGTGATCTTTGGGAGAAAGTTCTTAACCCTGATAATACCTACAGAAGGCAACTTATTGATCAGGTTGTATCTACAGCTMapped 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|86063114|gb|DR358871.1|DR358871EST: GAACTCATCAATGTCACCAACAAGAACTCTTTGTTCAAGTTACAAGCCAG GTACGTAGTGGAGAGGATGGATGG
genomic: GAACTCATCAATGTCACCAACAAGAACTCTTTGTTCAAGTTACAAGCCAGgtatttgatt ... ccaactgcagGTACGTAGTGGAGAGGATGGATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatattccacactagttactttgtagactacttacacacgattttccaactgcagGTACGTAGTGGAGAGGATGGATGGTGACCTCTGGGAGAAGGTTCTTACGGAAGAAAATGAATATAGGAGGCAACTTATAGACCAAGTTGTGTCTACTGCT
tacttac putative branch site (score: 1)
ttttcc putative PPT
ttacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttgattattgcttactagacttcttacttatattccacactagttactttgtagactacttacacacgattttccaactgcagGTACGTAGTGGAGAGGATGGATGGTGACCTCTGGGAGAAGGTTCTTACGGAAGAAAATGAATATAGGAGGCAACTTATAGACCAAGTTGTGTCTACTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA