Sequence
atgc intronic sequence ATGC exonic sequencegtaagcgaagaaagagaggaggacgcaaaaagcaaaggcgaccgagagtgctgagtgctattgcctgggcgctagcttcagtagttcagttccatcatgcacatcgacatgataaaaaagccgcgtcggttctttccttttcggaatcttgattggcgctgctgcttgttgcctgttggcacagTCGGGTGGGGCTCCTTCCAGCTGGGCTACTCCGGCAATGCGGATCTGGAGCCTGGGCGGTGCCGCCGGACGGACGGCAAGAAGTGGCGGTGCTCCAGGGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G853392_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g51970.1 (Oryza sativa), 3'ss of exon 1
gtaagcgaagaaagagaggaggacgcaaaaagcaaaggcgaccgagagtgctgagtgctattgcctgggcgctagcttcagtagttcagttccatcatgcacatcgacatgataaaaaagccgcgtcggttctttccttttcggaatcttgattggcgctgctgcttgttgcctgttggc---acagTCGGGTGGGGCTCCTTCCAGCTGGGCTACTCCGGCAATGCGGATCTGGAGCCTGGGCGGTGCCGCCGGACGGACGGCAAGAAGTGGCGGTGCTCCAGGGA
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-----------------gtaagccaagaaatgggaaaggaagcagatcaaccgaatgcttt---cttggctttagttcc----------tttcatcatggactgatatttatgataaaagctg----------ttccattccctgatcttggttg-cattgcccttggttgggtttttgctttgcagTGGGATGGGGATCTTTCCAGCTGGGCTACTCCGGCAGCGCGGATCCGGAGCCCGGCCGGTGCCGCCGGACGGACGGCAAGAAATGGCGGTGCTCGAGGGA
upper sequence: GRMZM5G853392_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ24024 (Selaginella moellendorffii), 3'ss of exon 2
gtaagcgaagaaagagaggaggacgcaaaaagcaaaggcgaccgagagtgctgagtgctattgcctgggcgctagcttcagtagttcagttccatcatgcacatcgacatgataaaaaagccgcgtcggttctttccttttcggaatcttgattggcgctgctg--cttgttgcctgttggcacagTCGGGTGGGGCTCCTTCCAGCTGGGCTACTCCGGCAATGCGGATCTGGAGCCTGGGCGGTGCCGCCGGACGGACGGCAAGAAGTGGCGGTGCTCCAGGGA
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----------------------------------------------------------------------gtgagtgcctgctgcc---tttctcccttcacttcactgctcgactgcctcctcgctg-ttctcagcaccttgcaccactggc-aactctaaagatctccttgctttcctgtgcagTGGGCTGGGGAAACTTCCACCTTGGAATTCCGAACAATCCCGACCCGGAGCCTGGTCGGTGCCGACGAACAGACGGCAAGAAGTGGAGGTGCTCCAGGGA
upper sequence: GRMZM5G853392_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ24588 (Selaginella moellendorffii), 3'ss of exon 2
gtaagcgaagaaagagaggaggacgcaaaaagcaaaggcgaccgagagtgctgagtgctattgcctgggcgctagcttcagtagttcagttccatcatgcacatcgacatgataaaaaagccgcgtcggttctttccttttcggaatcttgattggcgctgctg--cttgttgcctgttggcacagTCGGGTGGGGCTCCTTCCAGCTGGGCTACTCCGGCAATGCGGATCTGGAGCCTGGGCGGTGCCGCCGGACGGACGGCAAGAAGTGGCGGTGCTCCAGGGA
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----------------------------------------------------------------------gtgagtgcctgctgcc---tttctcccttcacttcactgctcgactgcctcctcgccg-ttctcagcaccttgcaccactggc-aactctaaagatctccttgctttcctgtgcagTGGGCTGGGGAAACTTTCACCTTGGAATTCCGAACAATCCCGACCCGGAGCCTGGTCGGTGCCGACGAACAGACGGCAAGAAGTGGAGGTGCTCCAGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctttccttttcggaatcttgattggcgctgctgcttgttgcctgttggcacagTCGGGTGGGGCTCCTTCCAGCTGGGCTACTCCGGCAATGCGGATCTGGAGCCTGGGCGGTGCCGCCGGACGGACGGCAAGAAGTGGCGGTGCTCCAGGGA
tcttgat putative branch site (score: 4)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcgaagaaagagaggaggacgcaaaaagcaaaggcgaccgagagtgctgagtgctattgcctgggcgctagcttcagtagttcagttccatcatgcacatcgacatgataaaaaagccgcgtcggttctttccttttcggaatcttgattggcgctgctgcttgttgcctgttggcacagTCGGGTGGGGCTCCTTCCAGCTGGGCTACTCCGGCAATGCGGATCTGGAGCCTGGGCGGTGCCGCCGGACGGACGGCAAGAAGTGGCGGTGCTCCAGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT