Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgctagtcctttgcccgaaaggtccacattaagttgttagagtcactgcttgtaacttagttttggcttctgtttacagTGGTGCACTTCATTTTACTGCGTCAAATAATGACTGTGGAGTTAGAGACTTTGACATGGAGAGATACCAGCTTGTTAAGCATTTCCGTTTTCCTTGGCCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13340.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13340.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os08g38880.3 (Oryza sativa), 3'ss of exon 5
gtttgtgctagtcctttgcccgaaaggtccacattaagtt---gttagagtcac--tgcttgtaacttagttttggcttctg---tttacagTGGTGCACTTCATTTTACTGCGTCAAATAATGACTGTGGAGTTAGAGACTTTGACATGGAGAGATACCAGCTTGTTAAGCATTTCCGTTTTCCTTGGCCA
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----gtactataacatcattttaaaaactactactttgtttaaaatgaagtgagaatgtatgaatcataacttcaaaaaatgaattatgcagTGGTTCGGTGCACTTCCTGGCTTCAAACAATGATTGTGGAGTTCGAGACTTTGACATGGAAAAATTTCAAATTTGCAATAATTTCCGTTTTCCTTGGGCT
upper sequence: AT3G13340.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G113726_T01 (Zea mays), 3'ss of exon 6
----------gtttgt--gctagtcctttgcccgaaaggtccacat-taagttgttagagtcactgcttg-taacttagttttggcttctgtttacagTGGTGCACTTCATTTTACTGCGTCAAATAATGACTGTGGAGTTAGAGACTTTGACATGGAGAGATACCAGCTTGTTAAGCATTTCCGTTTTCCTTGGCCA
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gtacttcatttttcgcaggcaaatcggttattctgtttatgaagagacaaaatgcatggatctcaacgtaatgacgtttgttgctcgtttctttgtagTGGTTCTCTGCACTTCCTTGCGTCAAACAATGATTGTGGACTTAGAGACTTTGACATGGAAAAGTTTCGAATATGCAACCACTTCCATTTTGCTTGGCCT
upper sequence: AT3G13340.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G12500.1 (Glycine max), 3'ss of exon 7
gtttgtgctagtcctttgcccgaaaggtcca-cattaagttgttagagtcactgcttgtaacttagtt---ttggcttctg-tttacagTGGTGCACTTCATTTTACTGCGTCAAATAATGACTGTGGAGTTAGAGACTTTGACATGGAGAGATACCAGCTTGTTAAGCATTTCCGTTTTCCTTGGCCA
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gtatatagttttccttctcctggtggttttgtcatttgatttatgga-tatcggcaccaagtttaatgtgattgttttctgatttttagTGGTGCAGTTCATTTCACAGCCGCTAATAATGATAGTGGAGTGAGAGACTTTGATATGGAGAAATTTCAGCTTTCTAAGCATTTTTGTTTTCCCTGGCCA
upper sequence: AT3G13340.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv19s0015g01750.t01 (Vitis vinifera), 3'ss of exon 6
gtttgtgctagtcctttgcccgaaaggtccacattaagttgttagagtcac---tgcttgtaacttagttttggcttct--gtttacagTGGTGCACTTCATTTTACTGCGTCAAATAATGACTGTGGAGTTAGAGACTTTGACATGGAGAGATACCAGCTTGTTAAGCATTTCCGTTTTCCTTGGCCA
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----gtacttggtgtttgcttatactagcaatgg-aacttgtcaattctgcatatgaacctaactcccattgcattttttaattttcagTGGTGCAGTTCACTTCATTGCCTCAAGTAATGACTGTGGAGTTAGAGACTTTGATATGGAAGATTTTCAACTTTCTAAGCACTTTCATTTTCCTTGGCCAMapped 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|47831951|gb|CK121635.1|CK121635EST: TATGATGATAATGCTATAACCAATGCTATTGAGATCTACAACAAACCCAG TGGTGCACTTCATTTTACTGCGTCAAATAATGACTGTGGAGTTAGAGACTT
genomic: TATGATGATAATGCTATAACCAATGCTATTGAGATCTACAACAAACCCAGgtttgtgcta ... ctgtttacagTGGTGCACTTCATTTTACTGCGTCAAATAATGACTGTGGAGTTAGAGACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacattaagttgttagagtcactgcttgtaacttagttttggcttctgtttacagTGGTGCACTTCATTTTACTGCGTCAAATAATGACTGTGGAGTTAGAGACTTTGACATGGAGAGATACCAGCTTGTTAAGCATTTCCGTTTTCCTTGGCCA
ttgtaac putative branch site (score: 2)
cttctgttt putative PPT
ttagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgctagtcctttgcccgaaaggtccacattaagttgttagagtcactgcttgtaacttagttttggcttctgtttacagTGGTGCACTTCATTTTACTGCGTCAAATAATGACTGTGGAGTTAGAGACTTTGACATGGAGAGATACCAGCTTGTTAAGCATTTCCGTTTTCCTTGGCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA