Sequence
atgc intronic sequence ATGC exonic sequencegtaagcccaacccgctctcctctctgctgcttcatcttgcacgcacgggcgaatgaatcgaattgacttctgcgcctggttgggttgcctgtgcttgttgctcctgcagTCAGCGTGAGTGAGGTCGAGGCGCTGTACGAGCTGTTTAAGAGGATCAGCAGCGCCGTCATTGATGATGGGCTGATTAACAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G173424_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 2
gtaagcccaacccgctctcctct---------------ctgctgcttcatcttgc----acgcacgggcgaatgaatcgaattgacttctgcgcctggttgggttg---cctgtgcttgttgctcctgcagTCAGCGTGAGTGAGGTCGAGGCGCTGTACGAGCTGTTTAAGAGGATCAGCAGCGCCGTCATTGATGATGGGCTGATTAACAAG
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gtaagtccgccgcattcgccattggttggggcgccgtactcctccttccttttgttgctgagcctgtctcattgggggaatttgactggtgtgtgtggttgggttggattttgtggccttgtgttgtgcagTCAGCGTGAGCGAGGTCGAGGCGCTGTACGAGCTCTTCAAGAAGATAAGCAGTGCTGTGATTGATGACGGGCTGATTAACAAG
upper sequence: GRMZM2G173424_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 3
------------gtaagcccaacccgctctcctctctgctgcttcatcttgcacgcacgggcg-----------aatgaat-cgaattgacttctgcgcctggttgg-gttgcctgtgcttgttgctcc--tgcagTCAGCGTGAGTGAGGTCGAGGCGCTGTACGAGCTGTTTAAGAGGATCAGCAGCGCCGTCATTGATGATGGGCTGATTAACAAG
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gtatgccctatcaccttctctactctttttttttttttttttttccggttataagattcgatgcaataccatttgaggaatgcaaaaatatttcttctgaagactattgatgattgaatttggttttggaatgcagTTAGTGTGAGTGAAATAGAAGCTCTTTATGAGCTTTTTAAGAAAATCAGCAGTGCCGTGATTGATGATGGGCTAATAAACAAG
upper sequence: GRMZM2G173424_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------------------gtaagcccaacccgctctcctctctgctgcttcatcttgcacgcacgggcgaatgaatcgaattgacttctgcgcctggttgggttgcctgtgcttgttgctcctgcagTCAGCGTGAGTGAGGTCGAGGCGCTGTACGAGCTGTTTAAGAGGATCAGCAGCGCCGTCATTGATGATGGGCTGATTAACAAG
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gtatgctctcaacttcttttccatcttattttaacttccatgcactttttttttccagttatatgtatgattcaaaggcttgcc-attactctagttgatgctctctgttaagaggaatgcaaatctttctttctgtgttttgatcattgactcgtttgggt---gcagTTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAG
upper sequence: GRMZM2G173424_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 1
gtaagcccaacccgctctcctctctgctgcttcatcttgcacgcacgggcgaatgaatcgaattgacttctgcgcctggttgggttgcctgtgcttgttgctcctgcagTCAGCGTGAGTGAGGTCGAGGCGCTGTACGAGCTGTTTAAGAGGATCAGCAGCGCCGTCATTGATGATGGGCTGATTAACAAG
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------tcattcctacctaatgctaatagtttgctttctgccaactcttttaatgaacc-attaaagcattgtactgaagattgtaattttt--ttctttccaatacagTTAGTGTAAGTGAAATCGAGGCACTATACGAGCTGTTTAAGAAGATCAGCAGCGCTGTGATTGATGACGGTCTGATCAACAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|60342172|gb|DN209145.1|DN209145EST: GCAGCCGCGGGGGCTCCAAGACCCCCAGGTCCTCGCGAGGGAGACCGTCT TCAGCGTGAGTGAGGTCGAGGCGCTGTACGAGCTGTTTAAGAGGATCAGCA
genomic: GCAGCCGCGGGGGCTCCAAGACCCCCAGGTCCTCGCGAGGGAGACCGTCTgtaagcccaa ... gctcctgcagTCAGCGTGAGTGAGGTCGAGGCGCTGTACGAGCTGTTTAAGAGGATCAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatcgaattgacttctgcgcctggttgggttgcctgtgcttgttgctcctgcagTCAGCGTGAGTGAGGTCGAGGCGCTGTACGAGCTGTTTAAGAGGATCAGCAGCGCCGTCATTGATGATGGGCTGATTAACAAG
aattgac putative branch site (score: 3)
ttgctcct putative PPT
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
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gtaagcccaacccgctctcctctctgctgcttcatcttgcacgcacgggcgaatgaatcgaattgacttctgcgcctggttgggttgcctgtgcttgttgctcctgcagTCAGCGTGAGTGAGGTCGAGGCGCTGTACGAGCTGTTTAAGAGGATCAGCAGCGCCGTCATTGATGATGGGCTGATTAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT