Sequence
atgc intronic sequence ATGC exonic sequence...aagctgtcaaccacatttttgttcaagtcatgatcagttttggcactatttttttttaacctctttcactaatgttgcactcttgtccaattgtgattagGACATTTGACATCAAAAAGTGATGTATACAGCTTTGGAGTAGTGCTACTTGAAATGCTCACAGGCCGGCGATCCATTGATAAGAAAAGACCAAATGGGGA
Basic information
species | Glycine max |
transcript | GLYMA19G02360.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 5
--aagctgtcaaccacatttttgttcaagtcatgatcagttttggcactatttttttttaacctctttcactaatgttgcactc---ttgtccaattgtga-ttagGACATTTGACATCAAAAAGTGATGTATACAGCTTTGGAGTAGTGCTACTTGAAATGCTCACAGGCCGGCGATCCATTGATAAGAAAAGACCAAATGGGGA
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ataatttgctatttattcacttgtttgag----aattaaact--gcaccacattcacttggtatattgcagtgttccaccacttcatcagttcatttctttctcagGTCACTTGACATCAAAGAGTGACGTGTACAGCTTTGGAGTGGTGCTACTGGAGATGATGTCAGGCAGAAGGTCAATGGACAAGAATAGGCCAAACGGTGA
upper sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 5
--------aagctgtcaaccacatttttgttcaagtcatgatcagttttggcactatttttttttaacctctttcactaatgttgcactcttgtccaattgtgattagGACATTTGACATCAAAAAGTGATGTATACAGCTTTGGAGTAGTGCTACTTGAAATGCTCACAGGCCGGCGATCCATTGATAAGAAAAGACCAAATGGGGA
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tgcaaatgaagtt--caaacacagatttgtt---gcctttggtattttatgcgat-tttcattatgactcttggtataattttcttgtattttttccacttt--tcagGCCATTTGACATCAAAGAGTGATGTCTATAGTTTTGGTGTGGTGCTACTTGAGATGATGTCAGGGCGCAGGTCAATGGACAAGAACCGCCCAAATGGTGA
upper sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 4
aagctgtcaaccacatttttgttcaagtcatgatcagttttggcactatttttttttaacctctttcactaatgttgcactcttgtccaattgtgattagGACATTTGACATCAAAAAGTGATGTATACAGCTTTGGAGTAGTGCTACTTGAAATGCTCACAGGCCGGCGATCCATTGATAAGAAAAGACCAAATGGGGA
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-----gtaagtca--gctatcttgaacttgtttttggttttcgcattatagat---tgagcttttgaact----tagaagttttaat--atgaacatcagGACATCTGACAACGAAGAGCGATGTATACAGTTTTGGAGTAGTTTTACTTGAAATATTAACTGGACGAAGATCTGTGGATAAAAGTCGGCCGAACGGGGAMapped 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|23063935|gb|BU578708.1|BU578708EST: AAGAGTTATGGGAACATATGGTTATGCTGCTCCTGAGTATGTGATGACTG GACATTTGACATCAAAAAGTGATGTATACAGCTTTGGAGTAGTGCTACTTG
genomic: AAGAGTTATGGGAACATATGGTTATGCTGCTCCTGAGTATGTGATGACTGgtgagttttg ... ttgtgattagGACATTTGACATCAAAAAGTGATGTATACAGCTTTGGAGTAGTGCTACTTG
EST:
gi|23733669|gb|BU765039.1|BU765039EST: AAGAGTTATGGGAACATATGGTTATGCTGCTCCTGAGTATGTGATGACTG GACATTTGACATCAAAAAGTGATGTATACAGCTTTGGAGTAGTGCTACTTG
genomic: AAGAGTTATGGGAACATATGGTTATGCTGCTCCTGAGTATGTGATGACTGgtgagttttg ... ttgtgattagGACATTTGACATCAAAAAGTGATGTATACAGCTTTGGAGTAGTGCTACTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctatttttttttaacctctttcactaatgttgcactcttgtccaattgtgattagGACATTTGACATCAAAAAGTGATGTATACAGCTTTGGAGTAGTGCTACTTGAAATGCTCACAGGCCGGCGATCCATTGATAAGAAAAGACCAAATGGGGA
cactaat putative branch site (score: 2)
tttttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagctgtcaaccacatttttgttcaagtcatgatcagttttggcactatttttttttaacctctttcactaatgttgcactcttgtccaattgtgattagGACATTTGACATCAAAAAGTGATGTATACAGCTTTGGAGTAGTGCTACTTGAAATGCTCACAGGCCGGCGATCCATTGATAAGAAAAGACCAAATGGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - -caaccac
- - - - - - - - - - - - - - catgatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcactc