Sequence
atgc intronic sequence ATGC exonic sequence...gaaattagaattgataagcatgcaaacatgattcctatagtgtctctggaaaggaaaaatataatggatatttgattaattttgctttttttttgtatagTTACCAGAAGTGGCATGCATATGGGCAATCAAAGCTTGCCAACATTTTACATGCCAACGAACTTACAAGACTTCTTAAA
Basic information
species | Glycine max |
transcript | GLYMA09G25080.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G25080.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g39670.1 (Oryza sativa), 3'ss of exon 3
gaaattagaattgataagcat-gcaaacatgattcctatagtgtctctggaaaggaaaaatataatg--gatatttgatt-aattttgctttttttttgtatagTTACCAGAAGTGGCATGCATATGGGCAATCAAAGCTTGCCAACATTTTACATGCCAACGAACTTACAAGACTTCTTAAA
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gtatgcaacttttatgcactttgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaatatatggttcaatcttgtgttgtacagGTACAACTCC----ATTGGA--GCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG
upper sequence: GLYMA09G25080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G009940_T02 (Zea mays), 3'ss of exon 4
gaaattagaattgataagcatgcaaacatgattccta---tagtgtctctggaaaggaaaaatataatggatatttgattaattttgctttttttttgtatagTTACCAGAAGTGGCATGCATATGGGCAATCAAAGCTTGCCAACATTTTACATGCCAACGAACTTACAAGACTTCTTAAA
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--gtatgtaattgctgtgc-tgtgattatgttctacggtctaatttactttgttttgaagaaaacc-tagccacttgttcaatcttgtgttgtgcagGTATAGT----AGCATTGG--TGCATATGGGCAATCAAAGCTTGCAAACATATTGCATGCTAATGAACTTGCCAGGCGATTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggaaaggaaaaatataatggatatttgattaattttgctttttttttgtatagTTACCAGAAGTGGCATGCATATGGGCAATCAAAGCTTGCCAACATTTTACATGCCAACGAACTTACAAGACTTCTTAAA
gattaat putative branch site (score: 3)
ttttgctttttttttg CT-rich tract
aaaaatataatggata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaattagaattgataagcatgcaaacatgattcctatagtgtctctggaaaggaaaaatataatggatatttgattaattttgctttttttttgtatagTTACCAGAAGTGGCATGCATATGGGCAATCAAAGCTTGCCAACATTTTACATGCCAACGAACTTACAAGACTTCTTAAA
- - - - - - - - - - - caaacat
- - - - - - - - - - - - - - - - - - - - - -ctctgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata