Sequence
atgc intronic sequence ATGC exonic sequence...tagttacaaaggtactcagctatgatgtatgccactgggataatgcatgttccaattgctttatttccattgtcaagatttacatggatttttaatgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATCAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
Basic information
species | Glycine max |
transcript | GLYMA09G04620.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 7
tagttaca-aaggtactcagctatgatgtatgccactgggataatgcatgttccaattgctttatttccattgtcaagatttacatggatttttaatgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATCAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
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ttatcacatgacttgaaaaagcaaaatgagt-caaaaactagatggctcataaaaaccgacagttactgactgtctactctgaattttggtaattatgcagATCTACATTCTTTTGTACAAGGAAGTTGCTCTTGCATTGAAAATCAACAGCTTGTACAGTAAACAAAAGCTACTTAACATTCATGAGAATGTAAAAGTTC
upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 7
tagttacaaaggtactcagctatgatgtatgccactgggataatgcatgttcca-attgctttatttccattgtcaagatttacat---ggattt-ttaatgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATCAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
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---gaaaaaaagaacacag--aaaatagcatcaaatggattcagactttctttataattacttattatcttggatgactttgaaattttgaattcatttttgcagATTTACATTCTCTTGTACAAGGAAGTTGCTCTTGCTTTGAAAATTAACAGCTTATACAGTAAACAGAGGCTACTTAACATTCATGAAAATGTTAAAGTTC
upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 8
---------------------------tagttacaaaggtactcagctatgatgtatgcc-----------actgggataatgcatgttccaattgctttatttccattgtcaag-------atttacatggatttttaatgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATCAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
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gtacttactacagaacatgcatgtacttaatagctattatcttctgttgtgaagcatgtctgtagtctgcaatggagatctgacttgtcaggtttggtggattactatctttcaactttttcatttttattactttctttttcagATATACATCCTTATCTACAAGGAGGTTGCTCTTGCTTTAAAGATCAACAGTGTATATAGCAAACGCAGGCTTCTTGGCATTCATGAGAATGTGCGGGTAC
upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 8
tagttacaaaggtact-cagctatgatgtatgccactggg-ataatgcatgttccaattgctttatttccattgtcaagatttacatggatttttaatgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATCAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
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-gaaatcattattcctgcatttttttttctttctgttgattatgggacctactttgatc-cactagaagggatgctggtgttaatttatcttatgactgcagATTTACATTCTTCTCTACAAAGAGGTTGCTCTTGCTTTGAAAATCAACAGTGTCTACAGTAAAAGGAAGCTTCTTAGCATTCATGAGAATGTGAGAGTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgttccaattgctttatttccattgtcaagatttacatggatttttaatgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATCAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
ttttaat putative branch site (score: 3)
ttttt CT-rich tract
atttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagttacaaaggtactcagctatgatgtatgccactgggataatgcatgttccaattgctttatttccattgtcaagatttacatggatttttaatgcagATTTACATTCTTCTCTACAAAGAGGTGGCTCTTGCTTTGAAAATCAACAGTGTTTATAGCAAGAAAAAGCTTCTTAGCATTCATGAGAATGTGAGGGTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - -agctatg
- - - - - - - - - - - - - gtatgcc
- - - - - - - - - - - - - - - - - - - - - - gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggat