Sequence
atgc intronic sequence ATGC exonic sequence...ttaaggcattttttttcttatatttcctgattgatagtttatttgtgtactaatttttttttgtttatattttctctatcaaaatatgattatgaactagCTGGTGTTGCAAGTGGAGCCACTAGAGCAGCTTTGACTCAGCATTTTGCTCTTCAGGATAATGCTGCAGATATATCTGCAAAG
Basic information
species | Glycine max |
transcript | GLYMA02G13010.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G13010.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g11500.1 (Oryza sativa), 3'ss of exon 8
ttaaggcattttttttcttatatttcctgattgatagtttatttgtgtactaatttttttttgtttatattttctctatcaaaatatgattatgaactagCTGGTGTTGCAAGTGGAGCCACTAGAGCAGCTTTGACTCAGCATTTTGCTCTTCAGGATAATGCTGCAGATATATCTGCAAAG
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gtaagcggatttacatgatgaatttcataaccttttaaattttcttttaa-aatgtttgttcgttaactaattatttgactatctgta---------tagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCGTTAACCCAGCATTTTGCACTTGCCAATAATGCAGCTGATATATCTGCAAAG
upper sequence: GLYMA02G13010.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G846548_T01 (Zea mays), 3'ss of exon 8
ttaaggcattttttttcttatatttcctgattgatagtttatttgtgtactaatttttttttgtttatattttctctatcaaaatatgattatgaactagCTGGTGTTGCAAGTGGAGCCACTAGAGCAGCTTTGACTCAGCATTTTGCTCTTCAGGATAATGCTGCAGATATATCTGCAAAG
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---------gtaagtttttgaattttagaagtcagaactcatgt---tgatgaacttcctgaggttat-tgggggctaatttattgtttctatgttctagCTGGTGTTGCTAGTGGAGCAACTAGAGCAGCACTAACGCAGCATTTTGCACTTGCAAATAATGCAGCTGATATTTCTGCAAAG
upper sequence: GLYMA02G13010.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G13770.2 (Arabidopsis thaliana), 3'ss of exon 7
--ttaaggcattttttttcttatatttcctgattgatagtttatttgtgtactaatttttttttgtttatattttctctatcaaaatatgattatgaactagCTGGTGTTGCAAGTGGAGCCACTAGAGCAGCTTTGACTCAGCATTTTGCTCTTCAGGATAATGCTGCAGATATATCTGCAAAG
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gtgcgtatcatttcttgcatcaaacattgaagttaagacttcggtt-tggattgatacatcggtttttaacttttttcaatc-----ttggctat----tagCTGGTGTTGCAAGTGGAGCAACCAGAGCAGCTCTAACACAGCACTTTGCTCTTCAAGACAATGCAGCGGATATATCTGCTAAG
upper sequence: GLYMA02G13010.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g00500.t01 (Vitis vinifera), 3'ss of exon 8
ttaaggcattttttttcttatatttcctgattgatagtttatttgtgtactaatttttttttgtttatattttctctatcaaaatatgattatgaactagCTGGTGTTGCAAGTGGAGCCACTAGAGCAGCTTTGACTCAGCATTTTGCTCTTCAGGATAATGCTGCAGATATATCTGCAAAG
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tattgtcagtggaattgaaaatacttctgctgaataagaataatgcacattgtgttgatatttctcatcaaaaatctaattttacactcttcaaaattagCTGGTGTTGCAAGTGGAGCAACTAGAGCTGCATTGACACAACATTTTGCTCTTCAAAATAATGCTGCAGATATATCTGCCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtactaatttttttttgtttatattttctctatcaaaatatgattatgaactagCTGGTGTTGCAAGTGGAGCCACTAGAGCAGCTTTGACTCAGCATTTTGCTCTTCAGGATAATGCTGCAGATATATCTGCAAAG
tactaat putative branch site (score: 1)
taatttttttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaaggcattttttttcttatatttcctgattgatagtttatttgtgtactaatttttttttgtttatattttctctatcaaaatatgattatgaactagCTGGTGTTGCAAGTGGAGCCACTAGAGCAGCTTTGACTCAGCATTTTGCTCTTCAGGATAATGCTGCAGATATATCTGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - ggcattt
- - - - - - - - - - - - -cctgatt
- - - - - - - - - - - - - - - - - - - - - -tgtgtac