Sequence
atgc intronic sequence ATGC exonic sequencegtatggattcctgcgttaggataagttctaaaagtatctgcttttgttcttatgtttcttgggttttgccttttgtttgttagACATATCTGCAATCTTTGACTGTACGGCTTGAGGAATGGAGATTGAAGAAGAGAGACACTGAGGAGTGGATGAGACATCGTCAACTTCCTGAAGAGTTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G30360.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G30360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g54760.1 (Oryza sativa), 3'ss of exon 5
gtatggattcc-tgcgttaggataagttctaaaa-gtatctgcttttgttcttatgtttcttgggttttgccttttgtttgttagACATATCTGCAATCTTTGACTGTACGGCTTGAGGAATGGAGATTGAAGAAGAGAGACACTGAGGAGTGGATGAGACATCGTCAACTTCCTGAAGAGTTGA
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gtaatttttaaatgtttagtgatcatgtctacactacgattgattcttttggcac-ttttttatacactgctactatttttccagACCTACTTGCAATCTATCACTGTGAGGGTTGAGGAATGGAGATTAAAACAAAGAGATACAGAGGAGTGGATGAGGCATCGTCAACTCCCACATGAACTAC
upper sequence: AT4G30360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G005791_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------------------gtatggattcctgcgttaggataagtt-ctaaaagtatctgcttttgttcttatgtttcttgggttttgccttttgtttgttagACATATCTGCAATCTTTGACTGTACGGCTTGAGGAATGGAGATTGAAGAAGAGAGACACTGAGGAGTGGATGAGACATCGTCAACTTCCTGAAGAGTTGA
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gtactttttatccactctactgcatactttatattgtacaggctttttatatgtgaacaataatactcgcttt-ggataatttattaattttgacataatttggaattttctgtcttacaacatgatgattattatcaagACCTACCTGCAATCTATTACTGTGAGGGTTGAGGAATGGAGATTAAAGCAAAGAGATACTGAGGAATGGATGAGACATCGTCAGCTTCCTTGTGAACTGC
upper sequence: AT4G30360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G30030.2 (Glycine max), 3'ss of exon 6
-------------gtatggat-tcctgcgttaggataagttctaaaagtatctgcttttgttcttatgtt--tcttgggttttgccttttgtttgt---tagACATATCTGCAATCTTTGACTGTACGGCTTGAGGAATGGAGATTGAAGAAGAGAGACACTGAGGAGTGGATGAGACATCGTCAACTTCCTGAAGAGTTGA
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ttgattagaataagtagcaatatactatactaata-gagtgctcagggttttt-ttttccttcttaatttgattttgcattgaggttgtttcttttgcgtagACATATTTGCAATCAATTACTATAAGGCTTGAGGAGTGGAGGCTTAAGCAAAGAGACACAGAGGAGTGGATGAGGCATCGCCAACTCCCTGAAGATTTGA
upper sequence: AT4G30360.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G24950.1 (Glycine max), 3'ss of exon 5
----gtatggattcctgcgttaggataagttctaaaagtatctgcttttgt--tcttatgtttc-ttgggttttgccttttgtttgtt----------agACATATCTGCAATCTTTGACTGTACGGCTTGAGGAATGGAGATTGAAGAAGAGAGACACTGAGGAGTGGATGAGACATCGTCAACTTCCTGAAGAGTTGA
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ttagcaatatactatactaatataatagagtgcctaggtttctttttatgttttcttctgtttaatttgattctgcattgaggttgttgctttggtgtagACTTATTTGCAATCAATTACTATAAGGCTTGAGGAGTGGAGGCTTAAGCGAAGAGACACAGAGGAGTGGATGAGGCATCGCCAACTCCCTGAAGATTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaaagtatctgcttttgttcttatgtttcttgggttttgccttttgtttgttagACATATCTGCAATCTTTGACTGTACGGCTTGAGGAATGGAGATTGAAGAAGAGAGACACTGAGGAGTGGATGAGACATCGTCAACTTCCTGAAGAGTTGA
ttctaaa putative branch site (score: 2)
ttttgccttttgttt putative PPT
ttatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggattcctgcgttaggataagttctaaaagtatctgcttttgttcttatgtttcttgggttttgccttttgtttgttagACATATCTGCAATCTTTGACTGTACGGCTTGAGGAATGGAGATTGAAGAAGAGAGACACTGAGGAGTGGATGAGACATCGTCAACTTCCTGAAGAGTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA