Sequence
atgc intronic sequence ATGC exonic sequencegtacaaagttttcgaacccttttggatgcacatattctgctgagtgctgatcgtcatttcaactaggtcaaatgattacaaaagacatttgcattgagatgttgcaaaataagttgatcatcattattttaaaagactaaaaggtaaataaactcattttctttctttctatgctccttgtagACAATTTATAGGAATTTTCAGAAGCTTACCCTCCAAGAGAGTCCAGGGATAGTTCCTGCAGGTCGACTTCCAAGATACAAGGAAGTGATACTATTAAATG
Basic information
species | Glycine max |
transcript | GLYMA17G03920.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 7
gtacaaagttttcgaacccttttggatgcacatattctgctgagtgctgatcgtcatttcaactaggtcaaatgattacaaaagacatttgcattgagatgttgca-aaataagttgatcatcattattttaaaagactaaaaggtaaataaactcattttctttctttctatgctccttgtagACAATTTATAGGAATTTTCAGAAGCTTACCCTCCAAGAGAGTCCAGGGATAGTTCCTGCAGGTCGACTTCCAAGATACAAGGAAGTGATACTATTAAATG
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-----------------------------------------gtaagttgcctgggacgatgg-tagttctgata--catttgggctttcttctctgtcttaatgcatgaacatgtttttggttctaatattcaaactgttctcttttaataa---cagttgatttatttgt------ctcacagACCATATATAGGAACTACCAGAAACTCACTCTTCAGGAAAGCCCAGGAATTGTTCCTGCTGGCAGGCTTCCAAGATACAAGGAAGTGATACTTCTGAATG
upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 5
gtacaaagttttcgaacccttttggatgcacatattctgctgagtgctgatcgtcatttcaactaggtcaaatgattacaaaagacatttgcattgagatgttgcaaaataagttgatcatcattattttaaaagactaaaaggtaaataaactcattttctttctttctatgctccttgtagACAATTTATAGGAATTTTCAGAAGCTTACCCTCCAAGAGAGTCCAGGGATAGTTCCTGCAGGTCGACTTCCAAGATACAAGGAAGTGATACTATTAAATG
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---------------------------------------------------------------------gtaggattctgta--atctctctatcattattttcctt--taactctacgaacttcaatgtaagttattggaatgtgaaattgaccatactgttaattact-cccttgtttcagACAATATACAGGAACTATCAGAAGCTTACAATCCAAGAGAGTCCAGGAACAGTGCCTGCTGGACGACTTCCAAGACACAAAGAAGTTATCCTGCTGAATG
upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 6
gtacaaagttttcgaacccttttggatgcacatattctgctgagtgctgatcgtcatttcaactaggtcaaatgattacaaaagacatttgcattgagatgttgcaaaataagttgatcatcattattttaaaagactaaaaggtaaataaactcattttctttctttctatgctccttgtagACAATTTATAGGAATTTTCAGAAGCTTACCCTCCAAGAGAGTCCAGGGATAGTTCCTGCAGGTCGACTTCCAAGATACAAGGAAGTGATACTATTAAATG
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---------------------------------------------------------------------------------aaatttttagtttcctttttttccaacctcgctggattatgaa-atggagccttaatgaaaaaagttcaaactcaattttggtttacatac-ctttttgcagACGATATACAGGAACTATCAAAAACTCACTCTCCAGGAGAGCCCAGGTATCGTGCCAGCAGGTCGTCTTCCTAGATACAAGGAAGTGATACTCTTGAACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaaagactaaaaggtaaataaactcattttctttctttctatgctccttgtagACAATTTATAGGAATTTTCAGAAGCTTACCCTCCAAGAGAGTCCAGGGATAGTTCCTGCAGGTCGACTTCCAAGATACAAGGAAGTGATACTATTAAATG
gactaaa putative branch site (score: 2)
ctcattttctttcttt putative PPT
taaataaactcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaaagttttcgaacccttttggatgcacatattctgctgagtgctgatcgtcatttcaactaggtcaaatgattacaaaagacatttgcattgagatgttgcaaaataagttgatcatcattattttaaaagactaaaaggtaaataaactcattttctttctttctatgctccttgtagACAATTTATAGGAATTTTCAGAAGCTTACCCTCCAAGAGAGTCCAGGGATAGTTCCTGCAGGTCGACTTCCAAGATACAAGGAAGTGATACTATTAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA