Sequence
atgc intronic sequence ATGC exonic sequencegtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 16
gtatgttcccaactttctataccttggttttgt-catactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
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----------gtatgctcgcttgttggtattgtgcttgcttgttattcctgca--aaatgcatt-ctcttgagtgggttaatgcttatagGTCAGGAGGCTCTCTGCATGTGAAACTATGGGTTCAGCCACAACAATTTGCAGCGACAAGACAGGAACGCTGACTTTGAATCAG
upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 15
gtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
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gtatgccaattgatgtttgtacttttagtcggttttg--acataaat--acatgtgaaactttgtttatattgtaacattgaattgtagGTAAGGAGGCTTTCTGCCTGCGAGACCATGGGCTCTGCCACAACCATATGCAGTGATAAGACTGGTACATTGACTATGAATCAG
upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 15
gtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG----
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gtatgccaatttttgtttgtgctttaggatttttgcatatct--atttgaga---aatgctgtttaatataac--acattgaattacagGTGAGGAGGCTTTCTGCCTGTGAGACAATGGGGTCAGCCACAACCATTTGCAGTGATAAGACTGGAACATTGACTATGAATCAGGTTA
upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 15
gtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
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gtatgccaattgatgtttgtacttataatcagttttg--acataaat--acatgtgaaactttgtttaatatgtcacattgaattgtagGTAAGGAGGCTTTCTGCCTGTGAGACCATGGGCTCTGCCACAACCATATGTAGTGATAAGACTGGCACATTGACCATGAATCAG
upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 18
gtatgttcccaactttctataccttgg--ttttgtcata-ctacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
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gtatgccaacttttgtttgtgctataggattttggcatatctatttga---gaaat--gctgtttgatataa-cacat----tgaattgcagGTGAGGAGGCTTTCTGCCTGTGAGACAATGGGGTCAGCCACAACCATTTGCAGTGATAAGACTGGAACATTGACTATGAATCAG
upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 18
gtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaat-gtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
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----gtaagtatcattttatgcatcaatctttttgttatttttagttt--taaggcatccttt-----ctaacagccaaggaatttgcagGTACGGCGGCTATCAGCCTGTGAAACTATGGGCTCTGCCACAACAATTTGCAGTGATAAGACAGGAACATTGACCTTAAATCAG
upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA07G00630.1 (Glycine max), 3'ss of exon 18
gtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
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----gtaagtatcattttatgcatctatctttttgttatttttagttt--taaggcatccttt-----ctaacagtaaaaaatttgcagGTACGGCGGCTATCGGCCTGTGAAACTATGGGCTCTGCCACAACAATTTGCAGTGATAAGACAGGAACATTGACCTTAAATCAG
upper sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 16
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 15
gtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
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-------gtaagaatcagaaggagtgttctcgctttagttctttcttcttggtt--attgtctgaccatttttctcaaatgccaaacagGTTAGAAGGCTTTCAGCTTGTGAAACCATGGGATCAGCAACAACAATCTGCAGTGACAAAACTGGAACTTTAACTTTGAATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
cgctcac putative branch site (score: 3)
cttcctat CT-rich tract
attgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttcccaactttctataccttggttttgtcatactacttgatccgacattgaatgctttgcacgctcacttcctatggaatgtagGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACAAGACTGGCACCTTAACTTTAAATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG