Sequence
atgc intronic sequence ATGC exonic sequence...gtctaagttgcagttcagaaaactaaaagtctagattgaatatcttttaattttatgtttatctgcatcctaagccagtagcttcatgtaatctgaacagATAGCTTCTTTGGCAATCCGAAGTGGGAATGGGCTTCTCTTGAAAGGAGGCAAGGAGGCTAAGCGATCAAATGCAATTTTGCACAAA
Basic information
species | Glycine max |
transcript | GLYMA18G03830.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G03830.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 10
gtctaagttgcagttcagaaaactaaaagtctagattgaatatcttttaattttatgtttatct-gcatcctaagccagtagcttcatgtaat-ctgaacagATAGCTTCTTTGGCAATCCGAAGTGGGAATGGGCTTCTCTTGAAAGGAGGCAAGGAGGCTAAGCGATCAAATGCAATTTTGCACAAA
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----------------gtaaaatgatttttttagttggaaagaaactgtatcagttaactacaaagcaacgttatttatcatattaacataacattgtacagATTGCATCTTTAGCAATCCGAAGTGGAAATGGTCTTCTCTTGAAAGGAGGAAAAGAAGCTATGAGATCAAACACAATACTGCATAAG
upper sequence: GLYMA18G03830.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv15s0024g00720.t01 (Vitis vinifera), 3'ss of exon 1
gtctaagttgcagttcagaaaactaaaagtctagattgaatatcttttaattttatgtttatctgcatcctaagccagtagcttcatgtaatctgaacagATAGCTTCTTTGGCAATCCGAAGTGGGAATGGGCTTCTCTTGAAAGGAGGCAAGGAGGCTAAGCGATCAAATGCAATTTTGCACAAA--------------
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-------------------------------------gtgtgcttctaattgtttttttttttttttgtctcaactagatgctcta--------gtgcagATGGCTACATTAGCAATCCGAAGTGG-AATAGACTTCTCTTGAAAAGTGGAAAAGAGGCCAAGCGATCTAATGCAATCTTGCACAAGGTTATAACTGAAGC
upper sequence: GLYMA18G03830.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 10
gtctaagttgcagttcagaaaactaaaagtctagattgaatatcttttaattttatgtttatctgcatcctaagccagtagcttc-------atgtaatctgaacagATAGCTTCTTTGGCAATCCGAAGTGGGAATGGGCTTCTCTTGAAAGGAGGCAAGGAGGCTAAGCGATCAAATGCAATTTTGCACAAA
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----gagctat--tacatggaattaaagttgtttgtttcttaattgttg-tgctattttccttatcattttaagtcaacatcatttttgggggtgtgatttgaacagATAGCTTCATTAGCAATCCGAAGTGGGAATGGACTTCTCTTGAAAGGTGGAAAAGAGGCCAAGCGATCTAATGCAATCTTGCACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaattttatgtttatctgcatcctaagccagtagcttcatgtaatctgaacagATAGCTTCTTTGGCAATCCGAAGTGGGAATGGGCTTCTCTTGAAAGGAGGCAAGGAGGCTAAGCGATCAAATGCAATTTTGCACAAA
ttttaat putative branch site (score: 3)
ttttatgtttatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctaagttgcagttcagaaaactaaaagtctagattgaatatcttttaattttatgtttatctgcatcctaagccagtagcttcatgtaatctgaacagATAGCTTCTTTGGCAATCCGAAGTGGGAATGGGCTTCTCTTGAAAGGAGGCAAGGAGGCTAAGCGATCAAATGCAATTTTGCACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - gttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgta