Sequence
atgc intronic sequence ATGC exonic sequencegtaatatttgtacactcagctatggtttctattttgtgcaatgtagactgtcttgttttcttgaagaccttttgatgtcggatgttcctcagttgccatttttattattgttaccattttttcagATGCCAATCGTTGGCAAGATGGAGCTATTGTAGCCAACAATCCTACGATCTTTGCCATTAGAGAAGCACAACTTTTGTGGCCAGATACACGAATAGATTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G451672_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g33670.1 (Oryza sativa), 3'ss of exon 11
gta-atatttgtacactcagctatggtttctattttgtgcaatg-tagactgtcttgttttcttgaagaccttttgatgtcggatgttcctcagttgccat----ttttattattgttaccattttttcagATGCCAATCGTTGGCAAGATGGAGCTATTGTAGCCAACAATCCTACGATCTTTGCCATTAGAGAAGCACAACTTTTGTGGCCAGATACACGAATAGATTG
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gtagatattcctaaacttagttgtggatattgttttgtgcaagaacagtaggcctctatttgtttgagtcctcaagatttgttatccaccgcagttcttatagccctttttttttcttcctttctcttcagACGTAAATCGTTGGCAGGATGGAGCTATTGTAGCCAACAATCCCACAATCTTTGCGATAAGAGAGGCACAACTTTTGTGGCCTGATACGAGAATAGATTG
upper sequence: GRMZM2G451672_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G01850.1 (Glycine max), 3'ss of exon 11
gtaatatttgtacactcagctatggtttctattttgtgcaatg--tagactgtcttgttttcttgaagaccttttgatgtcggatgttcctcagttgccatttttattattgttac--cattttttcagATGCCAATCGTTGGCAAGATGGAGCTATTGTAGCCAACAATCCTACGATCTTTGCCATTAGAGAAGCACAACTTTTGTGGCCAGATACACGAATAGATTG
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---------gtactgattactgtg----ctgttgtgtgcatcaatttggctgtattttagttttagttatttccatttctgtattgtttttttacatttatttattttcatcctgcaacgtgccttaagATGTCAACCGCTGGCAAGATGGTGCAATAGTGGCTAACAATCCTACAATTTTTGCCATAAGAGAAGCACAACTTCTGTGGCCTGATACAAAAATTGACTG
upper sequence: GRMZM2G451672_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 10
gtaatatttgtacactcagctatggtttctattttgtgcaatgtagactgtcttgttttcttgaagaccttttgatgtcggatgttcctcagttgccatttttattattgt-taccattttttcagATGCCAATCGTTGGCAAGATGGAGCTATTGTAGCCAACAATCCTACGATCTTTGCCATTAGAGAAGCACAACTTTTGTGGCCAGATACACGAATAGATTG
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---gtactgat-tactctgctgttgtttgcat------caat-taggctgtattttagttttagttatttccatttctgtattgttatttatgtgtatttattttcatcctgcaacatgccttaagATGTCAACCGCTGGCAAGATGGTGCGATAGTGGCTAACAATCCTACAATTTTTGCCATAAGAGAAGCACAACTTCTGTGGCCAGATACAAAAATTGACTG
upper sequence: GRMZM2G451672_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G61850.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaatatttgtacactcagctatggtttctattttgtgcaatgtagactgtcttgttttcttgaagaccttttgatgtcggatgttcctcagttgccatttttattattgttaccattttttcagATGCCAATCGTTGGCAAGATGGAGCTATTGTAGCCAACAATCCTACGATCTTTGCCATTAGAGAAGCACAACTTTTGTGGCCAGATACACGAATAGATTG
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---------------------------------gtctaccttctctattctccactcttatccatgactctttgttgtaagcttttacgctgatattatctt-gtttcctttctaaatcattaagACTCATATCGCTGGCAAGATGGTGCAATAGTGGCAAACAATCCTACAATCTTTGCCATCAGAGAAGCACAACTTCTATGGCCTGACACAAAAATTGATTG
upper sequence: GRMZM2G451672_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G61850.2 (Arabidopsis thaliana), 3'ss of exon 11
gtaatatttgtacactcagctatggtttctattttgtgcaatgtagactgtcttgttttcttgaagaccttttgatgtcggatgttcctcagttgccatttttattattgttaccattttttcagATGCCAATCGTTGGCAAGATGGAGCTATTGTAGCCAACAATCCTACGATCTTTGCCATTAGAGAAGCACAACTTTTGTGGCCAGATACACGAATAGATTG
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-------------------------gtacaagtcta--ccttctctattctccactcttatccatgactctttgttgtaagcttttacgctgatattatctt-gtttcctttctaaatcattaagACTCATATCGCTGGCAAGATGGTGCAATAGTGGCAAACAATCCTACAATCTTTGCCATCAGAGAAGCACAACTTCTATGGCCTGACACAAAAATTGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgatgtcggatgttcctcagttgccatttttattattgttaccattttttcagATGCCAATCGTTGGCAAGATGGAGCTATTGTAGCCAACAATCCTACGATCTTTGCCATTAGAGAAGCACAACTTTTGTGGCCAGATACACGAATAGATTG
ttttgat putative branch site (score: 4)
ccattttttc putative PPT
atttttattattgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatttgtacactcagctatggtttctattttgtgcaatgtagactgtcttgttttcttgaagaccttttgatgtcggatgttcctcagttgccatttttattattgttaccattttttcagATGCCAATCGTTGGCAAGATGGAGCTATTGTAGCCAACAATCCTACGATCTTTGCCATTAGAGAAGCACAACTTTTGTGGCCAGATACACGAATAGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC