Sequence
atgc intronic sequence ATGC exonic sequencegtgcgaaccttataaaattgtcgaaaggtggttccctgtttcttttgtgctttcctctgcataaagacggtattgatttctagacgactcttttaacagTGGTACCAAAAATTTACTAATGTTGATGATGTTATACCAATAAGTGCTAAATTTGGTCATGGAGTGGATGATATCAAGGAGTGGATATTGTCAAAGCTCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G158024_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g49220.1 (Oryza sativa), 3'ss of exon 4
gtgcgaaccttataaaattgtcgaaaggtggttccctgtttcttttgtgctttcctctgcataaagacggtattgatttctagacgactcttttaacagTGGTACCAAAAATTTACTAATGTTGATGATGTTATACCAATAAGTGCTAAATTTGGTCATGGAGTGGATGATATCAAGGAGTGGATATTGTCAAAGCTCC
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---------gtaaaatatcgttacaaaa--atttggagatggttttgtttttccctctacttc--gatgtaattgatttactggctacgattttcacagTGGTATCAAAAATTCACTAATGCTGATGACGTCATACCTATAAGTGCTAAATTTGGGCATGGAGTGGATGATATCAAGGAGTGGATATTATCAAAGCTCC
upper sequence: GRMZM2G158024_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G66470.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------------------gtgcgaaccttataaaat----------tgtcgaaaggtggttccctgtttcttttgtgctttcctctg----cataaagacggtat------tgatttctagacgactc---ttttaacagTGGTACCAAAAATTTACTAATGTTGATGATGTTATACCAATAAGTGCTAAATTTGGTCATGGAGTGGATGATATCAAGGAGTGGATATTGTCAAAGCTCC
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gtgagtatgctgtcgttgctatccttgaaccttggtaatactgtcctgttattaaaatcccaccattctagaatgaacttgcagtggtggaagatgcttcactataaacttgagatcaagatttggagtcatggtattgctatgttctttgcttaatagatgctgcaactccttgcagTGGTATGAAAAATTTACGGATGTTGATGAAGTTATACCTGTAAGTGCAAAGTATGGACATGGAATAGAGGATGTCAAAGAGTGGATATTATCCAAACTTC
upper sequence: GRMZM2G158024_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0023g02120.t01 (Vitis vinifera), 3'ss of exon 4
gtgcgaaccttataaaattgtcgaaaggtggttccctgtttcttttgtgctttcctctgcataaagacggtattgatttctag-----acgactcttttaacagTGGTACCAAAAATTTACTAATGTTGATGATGTTATACCAATAAGTGCTAAATTTGGTCATGGAGTGGATGATATCAAGGAGTGGATATTGTCAAAGCTCC
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acgcatatgttattagatcattactat---gcttcttaatcatggtgtgctaaaattcttactttga-actgtttattctgaatgagtatcattttcctttcagTGGTATGAGAAATTCATAGATGTTGATGAGGTCATACCAGTGAGTGCCAAGTATGGTCAAGGAGTAGATGATGTCAAGGATTGGATATTGTCAAAACTTCMapped 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|149086134|gb|EE175674.2|EE175674EST: TGAACAAGAAAGATCTCATAAAACCCGGAGAAATCGCAAAGAAACTTGAG TGGTACCAAAAATTTACTAATGTTGATGATGTTATAC
genomic: TGAACAAGAAAGATCTCATAAAACCCGGAGAAATCGCAAAGAAACTTGAGgtgcgaacct ... cttttaacagTGGTACCAAAAATTTACTAATGTTGATGATGTTATAC
EST:
gi|74240633|gb|DT648547.1|DT648547EST: TGAACAAGAAAGATCTCATAAAACCCGGAGAAATCGCAAAGAAACTTGAG TGGTACCAAAAATTTACTAATGTTGATGATGTTATACCAATAAGTGC
genomic: TGAACAAGAAAGATCTCATAAAACCCGGAGAAATCGCAAAGAAACTTGAGgtgcgaacct ... cttttaacagTGGTACCAAAAATTTACTAATGTTGATGATGTTATACCAATAAGTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgctttcctctgcataaagacggtattgatttctagacgactcttttaacagTGGTACCAAAAATTTACTAATGTTGATGATGTTATACCAATAAGTGCTAAATTTGGTCATGGAGTGGATGATATCAAGGAGTGGATATTGTCAAAGCTCC
tattgat putative branch site (score: 3)
ctctttt putative PPT
tattgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgaaccttataaaattgtcgaaaggtggttccctgtttcttttgtgctttcctctgcataaagacggtattgatttctagacgactcttttaacagTGGTACCAAAAATTTACTAATGTTGATGATGTTATACCAATAAGTGCTAAATTTGGTCATGGAGTGGATGATATCAAGGAGTGGATATTGTCAAAGCTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA