Sequence
atgc intronic sequence ATGC exonic sequencegtatgcacattttcacttctcactgtgctgcagtagaaagttacaacgccgcatgcgtgtcaaatcttataatttcaattagtccctgctgatttagcgtttcccttcaatctgaatacagCTTCTATGACCGTTCTGCTCCAATCTATACACAACCTCGACATCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAGGGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G163437_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 5
gtatgcacattttcacttct--cactgtgctgcagtagaaagttacaacgccgcatgcgtgtcaaatcttataatttcaattagtccctgctgatttagcgtttcccttcaatctgaatacagCTTCTATGACCGTTCTGCTCCAATCTATACACAACCTCGACATCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAGGGA
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----gtatgctttcaatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaa--tttataattgt------ctccttatgatataaaatataccatcaaaatatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGT
upper sequence: GRMZM2G163437_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 5
gtatgcacattttcacttctcactgtgctgcagtagaaagttacaacgccgcatgcgtgtcaaatcttataatttcaattagtccctgctgatttagcgtttcccttcaatctgaatacagCTTCTATGACCGTTCTGCTCCAATCTATACACAACCTCGACATCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAGGGA
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gtaaat-tatataggctatttaatata-tccatcatattgaca-aatgtatttcaacggtagtatattgtggttctgatgtttatgtgttcat---gcattttg--gcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
upper sequence: GRMZM2G163437_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 5
gtatgcacattttcacttctcactgtgctgca-gtagaaagttacaacgccgcatgcgtgtcaaatcttataatttcaattagtccctgctgatttagcgtttcccttcaatctgaatacagCTTCTATGACCGTTCTGCTCCAATCTATACACAACCTCGACATCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAGGGA
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----gtaaattgcctatttgatatatccatcatattgacaaatgtatttcaatgatagtgtt-----ttgtggttctgatgtttatgtgttcat---gcgttttg--gcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
upper sequence: GRMZM2G163437_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgcacattttcacttctcactgtgctgcagtagaaagttacaacgccgcatgcgtgtcaaatcttataatttcaattagtccctgctgatttagcgtttcccttcaat-ctgaatacagCTTCTATGACCGTTCTGCTCCAATCTATACACAACCTCGACATCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAGGGA
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---------------------------------------------gtacagtaaccgcatta----ctacactctctattgtatctgaatgattacttaacttatctgaattcttgatgcagTTTCTATGACCGTTCTGCTCCGATCTACACACAGCCGCGTTATTTACCACCGTCTAAGATGCTTGATGCTGATGTTACTGACAGTGTCATCGGAGAGGGC
upper sequence: GRMZM2G163437_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 5
gtatgcacattttcacttctcactgtgctgca-gtagaaagttacaacgcc------gcatgcgtgtcaaatcttataatttcaat-tagtccctgctgatttagcgtttcccttcaatctgaatacagCTTCTATGACCGTTCTGCTCCAATCTATACACAACCTCGACATCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAGGGA
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------gtagttttacagcccatcagactgtatactgtgaattttgatctctgttcaacagtttctttcattaccacatttctgatgcagtttatgata--ttaatatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttataatttcaattagtccctgctgatttagcgtttcccttcaatctgaatacagCTTCTATGACCGTTCTGCTCCAATCTATACACAACCTCGACATCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAGGGA
tgctgat putative branch site (score: 3)
tttcccttcaatct putative PPT
atttcaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcacattttcacttctcactgtgctgcagtagaaagttacaacgccgcatgcgtgtcaaatcttataatttcaattagtccctgctgatttagcgtttcccttcaatctgaatacagCTTCTATGACCGTTCTGCTCCAATCTATACACAACCTCGACATCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT