Sequence
atgc intronic sequence ATGC exonic sequencegttagtaatgtggttctcgtgaaaatacatgtattcgaaacttcaatttgtgacaagcatgataactctttctcctgttttcatgttttgcccttttgctttcctgattggttggttctcttgtacatgacaacatttaccttttttgcagGGCCTGTCATGACCAAATTTACAATTGCTTTAAGAGAAATTGGAACATACAAGGAAGTATTGCGCTCCCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 3
gttagtaatgtggttctcgtgaaaatacatgtattcgaaacttcaatttgtgacaagcatgataactctttctcctgttttcatgttttgcccttttgctttcctgattggttggttctcttgtacatgacaacatttaccttttttgcagGGCCTGTCATGACCAAATTTACAATTGCTTTAAGAGAAATTGGAACATACAAGGAAGTATTGCGCTCCCAG
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----------------------------------------------ttcaaaatagtgatcctagga--ttcagtaaatttcattccccagcttgttgccttcaaaattagt-gatcctttagtaagtg-tggcattcacttttttc-cagGACCCGTCATGACCAAATTTACAATTGCCCTGAGAGAAATTGGAACTTACAAGGAAGTATTGCGCTCACAG
upper sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 3
gttagtaatgtggttctcgtgaaaatacatgtattcgaaacttcaatttgtgacaagcatgataactctttctcctgttttcatgttttgcccttttgctttcctgattggttggttctcttgtacatgacaacatttaccttttttgcagGGCCTGTCATGACCAAATTTACAATTGCTTTAAGAGAAATTGGAACATACAAGGAAGTATTGCGCTCCCAG
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--------------------------------------cccttgtttttttaaccgtcacgc--attctttgaatagttaatacaacat-tacattcatttttgttattaatt------ttgataaactttga-gttggtattgt---cagGACCTGTCATGACCAAATTTTCTATTGCTTTGAGAGAAATCAGTACATACAAGGAACTTCTTCGGTCCCAG
upper sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 3
gttagtaatgtggttctcgtgaaaatacatgtattcgaaacttcaatttgtgacaagcatgataactctttctcctgttttcatgttttgcccttttgctttcctgattggttggttctcttgtacatgacaacatttaccttttttgcagGGCCTGTCATGACCAAATTTACAATTGCTTTAAGAGAAATTGGAACATACAAGGAAGTATTGCGCTCCCAG
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-----------------------------------------------ttgggactgacttcataatttgattttaagtctgtatgtt---acctttaactctaaaagtctaatggtgatgaaatgatttatgat-tgagtttctattccagGCCCTGTTATGACCAAATTCACCATAGCCTTAAGAGAAATTGGGACATATAAGGAAGTCCTTCGATCACAG
upper sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 3
gttagtaatgtggttctcgtgaaaatacatgtattcgaaacttcaatttgtgacaagcatgataactctttctcctgttttcatgttttgcccttttgctttcctgattggttggttctcttgtacatgacaacatttaccttttttgcagGGCCTGTCATGACCAAATTTACAATTGCTTTAAGAGAAATTGGAACATACAAGGAAGTATTGCGCTCCCAG
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-----------------------------------------------actaaactgacttcataatttgattttaagtctgtatgtt---acctttaactctaaaagtctaatggtgatgaaatgatttatgac-tgagtttctattacagGTCCTGTTATGACCAAATTCACCATAGCCTTACGAGAAATTGGTACATACAAGGAAGTTCTTCGATCACAG
upper sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G17300.1 (Glycine max), 3'ss of exon 4
gttagtaatgtggttctcgtgaaaatacatgtattcgaaacttcaatttgtgacaagcatgataactctttctcctgttttcatgttttgcccttttgctttcctgattggttggttctcttgtacatgacaacatttaccttttttgcagGGCCTGTCATGACCAAATTTACAATTGCTTTAAGAGAAATTGGAACATACAAGGAAGTATTGCGCTCCCAG
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----------------------------------------ccttgtttttt--taaccctcacgcattctttgaatattta-atataatattatattctttttt------gttagtaattttttataaactttgagttggtattat--cagGACCTGTCGTGACCAAATTTTCTATTGCTTTGAGAGAAATCAGTACATACAAGGAACTTCTTCGGTCCCAG
upper sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 3
gttagtaatgtggttctcgtgaaaatacatgtattcgaaacttcaatttgtgacaagcatgataactctttctcctgttttcatgttttgcccttttgctttcctgattggttggttctcttgtacatgacaacatttaccttttttgcagGGCCTGTCATGACCAAATTTACAATTGCTTTAAGAGAAATTGGAACATACAAGGAAGTATTGCGCTCCCAG
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----------------------------------------------------------gtctttactcgag-tcattttttctctttgttcctcctttttatctttcttgg--agtcatttctcaaggaactaagtta----tttgctcagGTCCTGTAATGACAAAATTCACTATTGCTCTACGAGAAATCGGGACATACAAGGAAGTACTTCGTTCTCAG
upper sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 3
gttagtaatgtggttctcgtgaaaatacatgtattcgaaacttcaatttgtgacaagcatgataactctttctcctgttttcatgttttgcccttttgctttcctgattggttggttctcttgtacatgacaacatttaccttttttgcagGGCCTGTCATGACCAAATTTACAATTGCTTTAAGAGAAATTGGAACATACAAGGAAGTATTGCGCTCCCAG
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-----------------------------------------tttaactggaaatt-gcatgata-----tggtactagctcc-tagaaggcctgttcataagtgaaatttactggcattgttg---atgaaatctctatttgtttcttcagGCCCTGTTATGACCAAATTCACTATTGCATTGAGAGAGATTGGGACATACAAGGAAGTTCTTCGCTCCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctttcctgattggttggttctcttgtacatgacaacatttaccttttttgcagGGCCTGTCATGACCAAATTTACAATTGCTTTAAGAGAAATTGGAACATACAAGGAAGTATTGCGCTCCCAG
tcctgat putative branch site (score: 3)
catttacctttttt putative PPT
aacattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtaatgtggttctcgtgaaaatacatgtattcgaaacttcaatttgtgacaagcatgataactctttctcctgttttcatgttttgcccttttgctttcctgattggttggttctcttgtacatgacaacatttaccttttttgcagGGCCTGTCATGACCAAATTTACAATTGCTTTAAGAGAAATTGGAACATACAAGGAAGTATTGCGCTCCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA