Sequence
atgc intronic sequence ATGC exonic sequence...ctgttacttttaacagctaatgcaatctggatgagtcacctatgaatgccatactggaatctgttgcgcttttgttgatcattattattttgcaatccagGCTAGGGGATCGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G542753_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S461_1V6.1 (Physcomitrella patens), 3'ss of exon 1
-ctgttacttttaacagctaatgcaatctggatgagtcacctatgaatgccatactggaatctgttgcgcttttgttgatc-attattattttgcaatccagGCTAGGGGATCGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
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cctgcaagcttaaaatgggggtggtttagggttttgaagttggttgatg--atgaggaagtttgagtcgtgttctgagttctgtttctcttgtgcgttttagGCTCGTGGTTTGAAGAAGCATCTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTTGACAAGTTGGGTGGTGCCTTC
upper sequence: GRMZM2G542753_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S2_16V6.1 (Physcomitrella patens), 3'ss of exon 1
ctgttacttttaaca--gctaatgcaatctggatgagtcacctatgaatgccatactggaatctgttgcgcttttgttgatcattattattttgcaatccagGCTAGGGGATCGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
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-tttcgtttacgtcattgttcgcttcatttttgtggtcggtttatcgactggattttggcctgtcatggtctcctgt-attcatctttccaatctctggcagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCCAGGCACTGGATGCTTGACAAGTTGGGTGGTGCCTTT
upper sequence: GRMZM2G542753_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S38_194V6.1 (Physcomitrella patens), 3'ss of exon 1
ctgttacttttaacag-ctaatgcaatctggatgagtcacctatgaatgccatactggaatctgttgcgcttttgttgatcattattattttgcaa-tccagGCTAGGGGATCGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
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ttatcggtttacgtaaacttgctttacttgtacgaagagtgcgtttgttcctgagtg--acgtgtggcttgttacgaactaattgttttcttgtgtctctagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCTCCCAGACATTGGATGCTTGACAAGTTGGGTGGTGCCTTC
upper sequence: GRMZM2G542753_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S81_172V6.1 (Physcomitrella patens), 3'ss of exon 1
-ctgttacttttaacagctaatgcaatctggatgagtcacctatgaatgccatactggaatctgttgcgcttttgttgatcatt--attattttgcaatccagGCTAGGGGATCGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
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gaggttggtttcg-tagc--atatttttgaaatgtgcgctgatttttttcttttttttatttttttacgttgtttttgttttttttgttatttttttcttcagGCTCGTGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAATTGGGTGGCGCCTTT
upper sequence: GRMZM2G542753_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S282_25V6.1 (Physcomitrella patens), 3'ss of exon 1
ctgttacttttaacagctaatgcaatctggatgagtcaccta--tgaatgccatactggaatctgttgcgcttttgttgatcattattattttgcaatccagGCTAGGGGATCGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
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atgctggagt-gagaatcagggtcttcggtattttgggactggctgatcaccctgttcaattggtacgtgtgctaaacatgtgttgcggtgttg-attccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGGATGCTTGACAAGCTGGGTGGCGCCTTC
upper sequence: GRMZM2G542753_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
ctgttacttttaacagctaatgcaatctggatgagtcacctatgaatgccatactggaatctgttgcgcttttgttga-tcattattattttgcaatccagGCTAGGGGATCGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
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----------------------------------------------------gtgagagcgcgcggctatcgcgggatcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgccatactggaatctgttgcgcttttgttgatcattattattttgcaatccagGCTAGGGGATCGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
tgttgat putative branch site (score: 4)
ttatttt putative PPT
ttttgttgatcattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgttacttttaacagctaatgcaatctggatgagtcacctatgaatgccatactggaatctgttgcgcttttgttgatcattattattttgcaatccagGCTAGGGGATCGAAGAAGCACTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAGCTTGGCGGAGCTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT