Sequence
atgc intronic sequence ATGC exonic sequence...tttggtttcttgaattttcatgtattatctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttattttttagATCACATACCACTTTTTCCATTGGAAGAAAGGGACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAACAAATGGATAATGGCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G558324_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g26940.2 (Oryza sativa), 3'ss of exon 1
----------tttggtttcttgaattttcatgtattatctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttattttttagATCACATACCACTTTTTCCATTGGAAGAAAGGGACACCTTTTGCTG---ATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAACAAATGGATAATGGCA
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agggcttgagttagatgtctacaatttgtagtcctcaacattcagctactagtactacatactgtatttaagtaaatttt----------attttaattttttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG---
upper sequence: GRMZM2G558324_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G42000.2 (Arabidopsis thaliana), 3'ss of exon 1
tttggtttcttgaattttcatgtattatctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttattttttagATCACATACCACTTTTTCCATTGGAAGAAAGGGACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAACAAATGGATAATGGCA
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-----------gtattattcccgatctcctccgatccaatttcgaaattgttggtttctagat-----ttgaatttttgagttt---ttttgttttctagGTCACGTATCATTCCTTCCATTGGAAGAAGGGAACACCATTTGGAGATGATCAAGGAGTCTATAATAGATTGACTTGGTGGGAACAGATTGATAATGGCA
upper sequence: GRMZM2G558324_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G01230.1 (Arabidopsis thaliana), 3'ss of exon 1
tttggtttcttgaattttcatgtattatctattaaacatttctctaagcaa-ctttgtccagataacacttgccatctggaat--gtgaatcttattttttagATCACATACCACTTTTTCCATTGGAAGAAAGGGACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAACAAATGGATAATGGCA
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-tggcattgcttgattgtca-aaaccaaat-ttaatctaatttctaattactctttaggaaaatgtgatgtctgagtagaaatttgtggatatttgttgtcagGTAACGTATCACAGCTTCCACTGGATGAAAGGAACTCCTTTTGCAGATGACCAAGGAATCTACAATGGTTTAACTTGGTGGGAACAAATGGACAATGGTC
upper sequence: GRMZM2G558324_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv15s0046g00140.t01 (Vitis vinifera), 3'ss of exon 1
tttggtttcttgaattttcatgtattatctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttattttttagATCACATACCACTTTTTCCATTGGAAGAAAGGGACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAACAAATGGATAATGGCA
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gtttgtttatcttctttgtctgtatacccttcctgatgctacattagattactttatatcctctctatgacctgattgaggagcatgcttcacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTGAAGACCAGGGAATCTACAATAGGTTGACGTGGTGGGAGCAGATAGACAATGGAA
upper sequence: GRMZM2G558324_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S123_9V6.1 (Physcomitrella patens), 3'ss of exon 1
--tttggtttcttgaattttcatgtattatctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttattttt--tagATCACATACCACTTTTTCCATTGGAAGAAAGGGACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAACAAATGGATAATGGCA
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atggtgagcaaaagattgttgttgtcttatttgtttttaatttaactcagaggttttgt---gttgtgttatgctggtttgcat-tggatttgattatgagcagGTTACTTACCGATTTTTCCATTGGAAGAAAGGGACTCCGTTCGCTGAAGACCAAGGTGATTATGGGAAGCTTACATGGTGGGAGCAAGTGGACGATGGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagcaactttgtccagataacacttgccatctggaatgtgaatcttattttttagATCACATACCACTTTTTCCATTGGAAGAAAGGGACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAACAAATGGATAATGGCA
agataac putative branch site (score: 3)
tcttatttttt putative PPT
tgaatcttatttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttggtttcttgaattttcatgtattatctattaaacatttctctaagcaactttgtccagataacacttgccatctggaatgtgaatcttattttttagATCACATACCACTTTTTCCATTGGAAGAAAGGGACACCTTTTGCTGATGACCAGGGAATGTACAACGCATTGACTTGGTGGGAACAAATGGATAATGGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG