Sequence
atgc intronic sequence ATGC exonic sequence...gatgtctgggcaatttcattcctgttgatttgttaggttgtccttgcttgatgcattttaccaactacactagtattacgtagtattggcacctgggcagGTTGGAGTGGAGGCAATGCATAAAGATAGCAAGTATGTATTATTTTTAGATGATGATGTTAGGCTACATCCTGGATCAATTGGAGCACTCGTTCGTGAAA
Basic information
species | Glycine max |
transcript | GLYMA01G01130.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G01130.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 5
gatgtctgggcaatttcattcctgttgatttg--ttaggttgtccttgcttgatgcattttaccaactacactagtattacgtagtattggcacctgggcagGTTGGAGTGGAGGCAATGCATAAAGATAGCAAGTATGTATTATTTTTAGATGATGATGTTAGGCTACATCCTGGATCAATTGGAGCACTCGTTCGTGAAA
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--tactgtggttactatatgttcatctcttggccttgttttattttttaccaaagaaggccagtaaattgactcgttactcatgtttatcaaactgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGATGATGATGTGAGGCTGCATCCTGGGACTATCGGAGCTCTCACAAAAGAAA
upper sequence: GLYMA01G01130.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------------------------gatgtctgggcaatttcattcctgttgatttgttaggttgtccttgct-tgatgcattttaccaactacactagtattacgtagtattggcacctgg-----gcagGTTGGAGTGGAGGCAATGCATAAAGATAGCAAGTATGTATTATTTTTAGATGATGATGTTAGGCTACATCCTGGATCAATTGGAGCACTCGTTCGTGAAA
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gtatgtatgattttttttttctcccaatattttttttatctctcctttgtgactgttcttaaatcaactgtaatcacaaccatgaaaagctaacttatcttccaacatacatttttcatttttgttgttcattcattggctttcgctgaatgttcctgtttctggcttctttttcttgaagATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTATTTTTGGATGATGATGTTAGACTGCATCCTGGAACAATCGGAGCTCTCACGACTGAGA
upper sequence: GLYMA01G01130.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 5
gatgtctgggcaatttcattcctgttgat--ttgttaggttgtccttgcttgatgcattttaccaactacactagtattacgtagtattggcacctgg-gcagGTTGGAGTGGAGGCAATGCATAAAGATAGCAAGTATGTATTATTTTTAGATGATGATGTTAGGCTACATCCTGGATCAATTGGAGCACTCGTTCGTGAAA
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-atatttgtatacacctgttccctgtaatggttgaagtatttttctagaatcatgtagtttttttg-tgctttatcat-gtatattctggttctctaatacagGTTGGGGTGGATAGAATGCATAAAGACAGCAAGTATGTATTATTCCTGGATGATGATGTCAGGCTGCATCCTGGGACCATTGGGGCCCTCGTTGCTGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttgatgcattttaccaactacactagtattacgtagtattggcacctgggcagGTTGGAGTGGAGGCAATGCATAAAGATAGCAAGTATGTATTATTTTTAGATGATGATGTTAGGCTACATCCTGGATCAATTGGAGCACTCGTTCGTGAAA
gcttgat putative branch site (score: 5)
tagtatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatgtctgggcaatttcattcctgttgatttgttaggttgtccttgcttgatgcattttaccaactacactagtattacgtagtattggcacctgggcagGTTGGAGTGGAGGCAATGCATAAAGATAGCAAGTATGTATTATTTTTAGATGATGATGTTAGGCTACATCCTGGATCAATTGGAGCACTCGTTCGTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
-atgtctg
- - - - - - - - cattcct
- - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaacta