Sequence
atgc intronic sequence ATGC exonic sequencegttttgtagttcaggaacttgttcttaccttgtttcttctgtttgaacttatttagttgacaaggtgagttatgcagGGTTGTTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGACAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G137118_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 3
gttttgtagttcaggaacttgttcttaccttgtttcttctgtttgaacttatttagttgaca-aggtgagttatgcagGGTTGTTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGACAT
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-gtttgtggattaggaacttactat-atctagcttatctggtttatacttatttagttgacatgggtcagtaatgcagGGTTGCTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGATAT
upper sequence: GRMZM2G137118_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 3
-----------------------------gtt-ttgtagttcaggaacttgttcttaccttgtttcttctgtt-tgaacttatttagttgacaaggtg--agttatg---cagGGTTGTTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGACAT
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gtgagagaccctttaagtttttgtgtaatgtaatcatagtcttaatagttactacagtattgaactctctgttgtaaactatttctgctaagcacattctacttctgttgcagGGTTGCTATGTCTGCATTGTCACTGGATACTGTGAAGGTGGAGACAT
upper sequence: GRMZM2G137118_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------gttttgtagttcagga--acttgttcttaccttgtttcttctgtttga-acttatttagttgacaaggtgagttatgcagGGTTGTTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGACAT
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gtgagccaaagcattgcgtttcgattgttattttgcagtatgcagtgttgtacgttctcctgtaaacttgaattagttgtattgtaatggttttatttatttattacttaagtatgtttttggttgtattgt--agGGTTGTTATGTTTGCATTGTTACTGGATACTGTGAAGGTGGAGACAT
upper sequence: GRMZM2G137118_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G09910.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------gttttgtagt-----tcaggaacttgttcttaccttgtttcttctgtttgaacttatttagttgacaaggtgagttat-gcagGGTTGTTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGACAT
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gtgaagacccttaaaatttttgtataatgtaatcatagacttagtttctttcagttaattgttaatagttacagtattgcaatctctgttgtgaactagaagtgtgagaataatgactgttt--acttttctgctaagcacattctactgttgcagGGTTGCTATGTCTGCATTGTCACCGGATACTGTGAAGGTGGAGACAT
upper sequence: GRMZM2G137118_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 3
----gttttgtagttcaggaacttgttcttaccttgtttct-tctgtttgaacttatttagttga--caaggt--gagttatgcagGGTTGTTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGACAT
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gtaagttttacatcactttgatttttatggatttaaagtagatttggttaaaggattttgataggagctagatttgaaaaatgcagGGTTGCTATGTTTGTATTGTCACTGGATACTGTGAAGGAGGAGACAT
upper sequence: GRMZM2G137118_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 3
-----------gttttgtagttcaggaacttgttcttaccttgtttcttctgt-ttgaacttatttagttgacaaggtgagttatgcagGGTTGTTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGACAT
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gtaggtcctggaaattctagttttttgacgaatttttttgctgtaaatgcgaccttgtactgaatcgagagctttgggttggaatgcagGGTTGCTATGTTTGCATTGTCACTGGATATTGTGAAGGAGGAGACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttaccttgtttcttctgtttgaacttatttagttgacaaggtgagttatgcagGGTTGTTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGACAT
tttgaacttattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttgtagttcaggaacttgttcttaccttgtttcttctgtttgaacttatttagttgacaaggtgagttatgcagGGTTGTTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA