Sequence
atgc intronic sequence ATGC exonic sequencegtgagtccttcttgtacttgcaagagatttagctttagtcaaatgccgagcaacagagtagggaggggactcaccactaattttgtgtttttttgctctgtgtatctacagGCTGATGCTGATGGTAATGGAACAATAGACTATGGCGAGTTTATCGCAGCCACAATGCATATCAACAGACTTGACAGAGAAGAACATCTTTACTCAGCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G12180.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G12180.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G08140.1 (Glycine max), 3'ss of exon 5
gtgagtccttcttgtacttgcaagagatttagctttagt-caaatgccgagcaacagagtagggaggggactcaccactaattttgtgtttttttgctctgtgtatctacagGCTGATGCTGATGGTAATGGAACAATAGACTATGGCGAGTTTATCGCAGCCACAATGCATATCAACAGACTTGACAGAGAAGAACATCTTTACTCAGCCT
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gtaagttgttcttaacaaaaaaaaggcaccaatttcaatattagttctagataaca-atcatttacaaa------catggattttctgattctt----ctacaaat-tacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCACATGAACAGAATGAACAGAGAAGAACATCTTTACACTGCCT
upper sequence: AT5G12180.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G36000.1 (Glycine max), 3'ss of exon 5
gtgagtccttcttgtacttgcaagagatttagctttagtcaaatgccgagcaacagagtagggaggggactcaccactaattttgtgtttttttgctctgtgtatctacagGCTGATGCTGATGGTAATGGAACAATAGACTATGGCGAGTTTATCGCAGCCACAATGCATATCAACAGACTTGACAGAGAAGAACATCTTTACTCAGCCT
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gtaagttattctt---caccaaaaaaccatagcaccaatttcagtagtacttctagatcactgttatttacagacatggattttctcattctt----ctacaaat-tacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCAAATGAACAGAATGAACAGAGAAGAACATCTTTATACTGCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtagggaggggactcaccactaattttgtgtttttttgctctgtgtatctacagGCTGATGCTGATGGTAATGGAACAATAGACTATGGCGAGTTTATCGCAGCCACAATGCATATCAACAGACTTGACAGAGAAGAACATCTTTACTCAGCCT
cactaat putative branch site (score: 2)
taattttgtgtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtccttcttgtacttgcaagagatttagctttagtcaaatgccgagcaacagagtagggaggggactcaccactaattttgtgtttttttgctctgtgtatctacagGCTGATGCTGATGGTAATGGAACAATAGACTATGGCGAGTTTATCGCAGCCACAATGCATATCAACAGACTTGACAGAGAAGAACATCTTTACTCAGCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC