Sequence
atgc intronic sequence ATGC exonic sequencegttagtttgccaaccagtgcattgtagttgacatgcacaacttcgttcagcctttaatcttgatcccaatattcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 3'ss of exon 2
gttagtttgccaaccagtgcattgtagttgacatgcacaacttcgtt--cagcctttaatcttgatcccaatattcttat--cagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
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gttagtcggcgaaacagcgcgatttgctcacaccacatgatgtagtttctagtctctaatctcgattgtaacattcttatttcagGATTCGGAACTGTCTGGTTCAGCTTTATTCAAAGGATATCACTCCAGATGACAAGCAAGAGCTTGATGAGGCTCTCCAGAGAGAG---------------
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 2
---------gttag--tttgccaaccagtgcattgtagttgacatgc--acaacttc---gttcagcct--ttaatcttgatcccaat-attcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
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atctgtaatgacaggacatggtatatagtatactatttctagcattgtggcaatttctgcattgaggctaattatttctgttggtgatcattctcttcagGATAAGGAATTGTTTGACACAATTATATGCTAAGGACATAACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG---------------
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G09810.1 (Glycine max), 3'ss of exon 3
-----------------gttagtttgccaaccagtgcattgt-agttgacatgcacaacttcgttcagcctttaatcttgatcccaa--tattcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
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gtttgtatcatgttttttcccccctcttttctgttgctttatgaatagatttacagagaagtgaaggaaactaagttctcatgtggtcctcttccttacagGATAAGAAATAATTTAACTCAGTTGTATGCCAAAGACATCACTCCTGATGATAAGCAGGAACTTGACGAGGCTCTACAGAGGGAG---------------
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 3
-----------------------------gttagtttgccaaccagtgcattgtagttgacatgcacaacttcgtt--cagcctttaatctt--gatcccaatattcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
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gtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttcttttttaaagctgttgcatagttaacaaaattgagccttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATCACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG---------------
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G36670.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------------------gttagtttgccaaccagtgcattgtagttgacatgc--acaacttc---gttcagcct--ttaatcttgatcccaat-attcttatcagGATACGCAA--CTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
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gtagttcattcattgttgcattttttatacatttgaaaatggaaatcattgacctgtaatgacaggacatgatatatatagactatagtataccatttctggcattgtggcaatttctgcattgagactaattatttctgttggtgatcattctcttcaggataaagGAATTTGTTTGACACAATTATATGCTAAGGACATTACACCAGATGATAAGCAGGAACTTGATGAGGCTTTACAAAGAGAG---------------
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G33380.1 (Glycine max), 3'ss of exon 2
--------------gttagtttgccaaccagtgcattgt-agttgacatgcacaacttcgttcagcctttaatcttgatcc--caatattcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
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gtttgtatcgagttttttttctctcttttgtttctttatgaatagatttactcagaagtgaaggaatttaaattttcatgtgttcctctgccttacagGATAAGAAATAATTTAACTCAGTTGTATGCCAAAGACATTACTCCTGATGATAAGCAGGAACTTGATGAGGCTCTACAGAGGGAG---------------
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G35840.1 (Glycine max), 3'ss of exon 2
------------------------------------gttagtttgccaaccagtgcattgtagttgacatgca-caacttcgtt--cagcctttaatctt--gatcccaatattcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
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gtttgttacaaaatatagtatttttcagcttcagtattcacttttgtattttctttttttaagtttttgcatagtcacatagttaacaaaattgagctttatggttttcatctgcattgcagGATAAGGAATTGTTTATCTCAATTGTATGCCAAAGACATTACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG---------------
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT3G14940.1 (Arabidopsis thaliana), 3'ss of exon 3
gttagtttgccaaccagt-gcattgtagttgacatgc-acaacttcgttca---gcctttaatcttgatcccaatattcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
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gttagtttttgacttagttgttttctggagagagtgagaaaactctgtttgcttgtgtgttgacctgacattaaatgttttctcagGATAAGGGACTGTCTTGCTCAACTCTATGCAAAGGACATTACTCCTGATGACAAGCAGGAGCTAGATGAGTCTCTGCAAAGAGAG---------------
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv12s0028g02180.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------gttagtttgccaaccagtgcattgtagttgacatgcaca---acttcgttcagcctttaatc------ttgatcccaatattcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
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gtttgttctccagttaccgtaatatttttattcttgtaaacgtaagagagggaaaagggttatttgcttcacataggctcttgttgatgctttgtttttccttcccttttcagGATAAGGAATTGCTTGGCCCAGTTATATGCTAAGGACATCACTCCTGATGATAAGCAAGAGCTTGATGAGGCTTTACAAAGAGAG---------------
upper sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 2
gttagtttgccaaccagtgcattgtagttgacatgcacaacttcgttcagcctttaatcttgatcccaatattctta----tcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
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gtttgtaatcaaattcctgcccttttgttcttgcactataattttttctctcctttttttcacctctcttatttcttctactcagGATCCGGAACTGTTTAGCCCAGTTATATGCCAAAGACATTACTCCTGATGATAAGCAGGAACTTGATGAGGCTCTACAGAGAGAG--------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgacatgcacaacttcgttcagcctttaatcttgatcccaatattcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
tcttgat putative branch site (score: 4)
ttcttatc putative PPT
aatattcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttgccaaccagtgcattgtagttgacatgcacaacttcgttcagcctttaatcttgatcccaatattcttatcagGATACGCAACTGTTTGGTTCAACTCTACTCAAAAGATATCACTCCGGATGATAAGCAGGAACTTGATGAGGCTCTGCAAAGAGAGGTACTTCTTTCAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG