Sequence
atgc intronic sequence ATGC exonic sequencegtaatcatctgcattttcagttgacggtttgattgatacttgaaagttaccacttaccccttaattggtgatctaagtatactcagctatctgattgtggaacaggacactgaattattagagatgctgttgagctgattatattttttattttgcagGGTGAGCTATTTGAGATTCTTGAGGATGATAAGTGCCTTCCGGAAGAGCAAGTTCAAGCAATTGCAAAACAATTG
Basic information
species | Glycine max |
transcript | GLYMA20G16860.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G16860.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g24550.1 (Oryza sativa), 3'ss of exon 4
gtaatcatctgcattttcagttgacggtttgattgatacttgaaagttaccacttaccccttaattggtgatctaagtatactcagctatctgattgtggaacaggacactgaattattagagatgctgttgagctgattatattttttattttgcagGGTGAGCTATTTGAGATTCTTGAGGATGATAAGTGCCTTCCGGAAGAGCAAGTTCAAGCAATTGCAAAACAATTG
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-----------------------------------------------------gtacaggttgatttttcagtgtagttttcaccaacaattggttttgcagtggaat--ttagttg-----------gttaaacttcatatataatggttgtctcagGGAGAGCTGTTTGAGGTGCTTGAGGATGATAAGTGCCTTCCAGAAGAACAGGTTCAAGCAATTGCTAAGCAGCTG
upper sequence: GLYMA20G16860.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G062524_T02 (Zea mays), 3'ss of exon 3
gtaatcatctgcattttcagttgacggtttgattgatacttgaaagttaccacttaccccttaattggtgatctaagtatactcagctatctgattgtggaacaggacactgaattattagagatgctgttgagctgattatattttttattttgcagGGTGAGCTATTTGAGATTCTTGAGGATGATAAGTGCCTTCCGGAAGAGCAAGTTCAAGCAATTGCAAAACAATTG
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-----------------------------------------------------gtacacaagaact--cagtttgattaccttgtcctttctcatctttgactggt---ttcaattgtttgcagctggctaactctaatgaaaatgcttgtct--cagGGAGAACTGTTTGAGGTGCTCGAGGATGATAAATGCCTTCCAGAAGAACAAGTTCAGGCAATTGCTAAGCAGCTG
upper sequence: GLYMA20G16860.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G50240.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaatcatctgcattttcagttgacggtttgattgatacttgaaagttaccacttaccccttaattggtgatctaagtatactcagctatctgattgtggaacaggacactgaa-ttattagagatgctgttgagctgattatattttttattttgcagGGTGAGCTATTTGAGATTCTTGAGGATGATAAGTGCCTTCCGGAAGAGCAAGTTCAAGCAATTGCAAAACAATTG
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-------------------------------------------------gtacttttctc---actgtagattgtagaat-ctaaagtactgatttatgaagcatatagctagacttatatgaaataaagaatcacc-atggaacacccaattttacagGGTGAATTGTTTGAGATTCTTGAAGATGACAAGTGCCTTCCCGAAGAGCAAGTTCAAGCAATCGCAAAGCAATTG
upper sequence: GLYMA20G16860.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 3
---------------gtaatcatctgcattttcagttgacggtttg-attgatacttgaaagtt-accacttaccccttaat-tggtgatctaagtatactcagctatctgattgtggaacaggaca--ctgaattatt--------ag---agatgc-tgttgagctgattatattttttattttgcagGGTGAGCTATTTGAGATTCTTGAGGATGATAAGTGCCTTCCGGAAGAGCAAGTTCAAGCAATTGCAAAACAATTG
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gtaattagctcttctctctctctctctctctctcttctctgttttgtacttacacatgcaaattcattccatgcgcatctatgcagcagaaagaatgt-ttcagagatgc-accctaacacaaaatatgcttggttattttgaccatagtttagatgcatgagtagttaatgaaaattttccatatgcagGGAGAACTCTTTGAGATTCTTGAGGATGACAAGTGCCTTCCTGAAGAACAAGTTCAAGCAATTGCAAAGCAGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggacactgaattattagagatgctgttgagctgattatattttttattttgcagGGTGAGCTATTTGAGATTCTTGAGGATGATAAGTGCCTTCCGGAAGAGCAAGTTCAAGCAATTGCAAAACAATTG
agctgat putative branch site (score: 4)
ttttttatttt putative PPT
agctgattatattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcatctgcattttcagttgacggtttgattgatacttgaaagttaccacttaccccttaattggtgatctaagtatactcagctatctgattgtggaacaggacactgaattattagagatgctgttgagctgattatattttttattttgcagGGTGAGCTATTTGAGATTCTTGAGGATGATAAGTGCCTTCCGGAAGAGCAAGTTCAAGCAATTGCAAAACAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA