Sequence
atgc intronic sequence ATGC exonic sequencegttctagaagcactaacttttttgtatctatgaatcttgtttaagactttaggaactatttgctgtgtcaattattcttacttttttttggaatatcttcagGACCCGGCAGAAGCTGATAAGCTGTTGAAAATCCAGAGGGAATTGGATGAGACCAAGATTATCCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G58180.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G58180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 3
-------gttctagaagcactaacttttttgtatctatgaatcttgtttaagactttaggaactatttgctgtgtcaattattcttacttttttttggaatatcttcagGACCCGGCAGAAGCTGATAAGCTGTTGAAAATCCAGAGGGAATTGGATGAGACCAAGATTATCCTT
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tcttcttgtccttgttggtccaaactgccagtacttaaaca-cgcactgcatcctgcatgaatgttttcttatg--agataacttgatttcattat------tttgtagGACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA
upper sequence: AT5G58180.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 3
----------------------gttctagaagcactaacttttttgtatctatgaatcttgtttaagactttaggaac-tatttgc-------tgtgtcaattattcttacttttttttggaatatcttcagGACCCGGCAGAAGCTGATAAGCTGTTGAAAATCCAGAGGGAATTGGATGAGACCAAGATTATCCTT
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gcatataaatacccctttttatgttgtctggcaaaacaattgtttgattttctaaattgtgtt--acattctgctaacctttttacacaagtatgactcaaacccctttatctgttcctgtcaaatcttcagGATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaggaactatttgctgtgtcaattattcttacttttttttggaatatcttcagGACCCGGCAGAAGCTGATAAGCTGTTGAAAATCCAGAGGGAATTGGATGAGACCAAGATTATCCTT
ttcttac putative branch site (score: 2)
tatcttc putative PPT
aattattcttactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctagaagcactaacttttttgtatctatgaatcttgtttaagactttaggaactatttgctgtgtcaattattcttacttttttttggaatatcttcagGACCCGGCAGAAGCTGATAAGCTGTTGAAAATCCAGAGGGAATTGGATGAGACCAAGATTATCCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT