Sequence
atgc intronic sequence ATGC exonic sequence...ctacgtttctatttgtaatatatgaaccattagcagtactggtaggcaatgctatgaattgataattcatcttaaaactgagccaatggagctgtcgcagGTTTCAAACATGCTCCCCTTACTGAAACGCGGCATTGGCGTGCATCATTCTGGTCTGTTGCCTATTTTAAAGGAAGTCATTGAGATACTCTTTCAGGAGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G040995_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g18140.1 (Oryza sativa), 3'ss of exon 5
--ctacgtttctatttgtaatatatgaaccattagcagtactggtaggcaatgctatgaattgataattcatcttaa-aactgagccaatggagctgtcgcagGTTTCAAACATGCTCCCCTTACTGAAACGCGGCATTGGCGTGCATCATTCTGGTCTGTTGCCTATTTTAAAGGAAGTCATTGAGATACTCTTTCAGGAGG
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taattggtccataccttcaaccggtg--cttgtattttatctttcatttagttcctttgataactgagcgattgggataattgagcca-tggggttttcacagGTTTCAAACATGCTTCCCTTGTTGAAACGTGGCATTGGTGTACATCATTCTGGTCTTTTGCCCATTTTGAAGGAAGTGATTGAGATACTCTTCCAAGAGG
upper sequence: GRMZM2G040995_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G47700.1 (Glycine max), 3'ss of exon 5
--------------------------------------ctacgttt-ctatttgt-aatatatgaaccattagcagtactggtaggcaatgctatga-attgataattcatcttaaaactgagccaa-tggagctgtcgcagGTTTCAAACATGCTCCCCTTACTGAAACGCGGCATTGGCGTGCATCATTCTGGTCTGTTGCCTATTTTAAAGGAAGTCATTGAGATACTCTTTCAGGAGG
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gtacctgcccttgaatcctcccaaaacttgtttgatgattaagcttgctgtttcttaacaccactgctttctgaccaactgtctagaaatacaattttagttgcatgttgtgtcacttttaaggtatctttattttttttagGTTTCAAACATGCTGCCCTTGCTGAAACGTGGAATAGGAGTACATCACTCTGGTTTACTCCCAATTCTAAAGGAAGTGATTGAGATCTTATTTCAAGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaatgctatgaattgataattcatcttaaaactgagccaatggagctgtcgcagGTTTCAAACATGCTCCCCTTACTGAAACGCGGCATTGGCGTGCATCATTCTGGTCTGTTGCCTATTTTAAAGGAAGTCATTGAGATACTCTTTCAGGAGG
aattgat putative branch site (score: 4)
aattgataattcatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctacgtttctatttgtaatatatgaaccattagcagtactggtaggcaatgctatgaattgataattcatcttaaaactgagccaatggagctgtcgcagGTTTCAAACATGCTCCCCTTACTGAAACGCGGCATTGGCGTGCATCATTCTGGTCTGTTGCCTATTTTAAAGGAAGTCATTGAGATACTCTTTCAGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA