Sequence
atgc intronic sequence ATGC exonic sequencegtaccggacagtagttccttctgttgtcataccagtgttggggaaaaataaaacaaaacctaccacggtgccccccgcccgtaacgttgttgtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCCTCTACATGACGTACAGCGGCGAGAACACCTTCGGGCTGTTCTGAGTGGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G134613_T08 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g09240.1 (Oryza sativa), 3'ss of exon 5
gtaccg-gacagtagttccttctgttgtcataccagtgttggggaaaaataaaacaaaacctaccacggtgccccccgcccgtaacgttgttgtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCCTCTACATGACGTACAGCGGCGAGAACACCTTCGGGCTGTTCTGAGTGGG-
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gtatggcaatatgagctctgggagcactcagttcaacatcaacataaaaaaaaatcataattgc-gtgatccctaaaatgccttgttgcattgctcctacagCTGCCCTGATGTCCGCTATCTATGAGGAGAACAAGGATGAGGACGGCTTCCTCTACATGACCTACAGCGGGGAGAACACCTTCGGCCTGTT-TGTCTGAGT
upper sequence: GRMZM2G134613_T08 (Zea mays), 3'ss of exon 1
lower sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 4
gtaccggacagtagttccttctgttgtcataccagtgttggggaaaaataaaacaaaacctaccacggtgcccc-ccgcccgtaacgttgttgtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCCTCTACATGACGTACAGCGGCGAGAACACCTTCGG-GCTGTTCTGAGTGGG-
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-cagcagg-gccagagccgggcgctgtggcaccgccgtgtgcaccgtcgctgtctttgctcaccacgtccttgcgcccctccttgcaacccactcctcacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGGTGCCGGG--GAGCAGCT
upper sequence: GRMZM2G134613_T08 (Zea mays), 3'ss of exon 1
lower sequence: PP1S249_49V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaccggacagtagttccttctgttgtcataccagtgttggggaaaaat----aaaacaaaacctaccacggtgccccccgcccgtaacgttgttgtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCCTCTACATGACGTACAGCGGCGAGAACACCTTCGG-GCTGTTCTGAGTGGG
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----ttgattctagt-ctgtgtattattgcactgctgttgtgtgggatttgttgatgggttacttaattcattgaatgtcgcaccattcaactttgtttgtgcagCTGCTATGATGTCATCCATTTACGATGAACACAAGGATGAGGACGGATTCCTGTACTTTACTTACAGTGGTGAAAACACCTTCGGAGATGTTATCAACTG-
upper sequence: GRMZM2G134613_T08 (Zea mays), 3'ss of exon 1
lower sequence: EFJ09352 (Selaginella moellendorffii), 3'ss of exon 4
gtaccggacagtagttccttctgttgtcataccagtgttggggaaaaataaaacaaaacctaccacggtgccccccg-cccgtaacgttgttgtccct--gcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCCTCTACATGACGTACAGCGGCGAGAACACCTTCGGGCTGTTCTGAGTGGG-
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------------------------------------------gtatgagccgtcgagacgtaatcccacgtatattgatttacactgttcctttccttttgtagCGGCATTGATATCGACCATCTACGAGGAGCACAAGGACGAGGATGGATTCCTCTACTTCACGTACAGCGGGGAGAATACCTTCGG-CCAAGAAGAACACTA
upper sequence: GRMZM2G134613_T08 (Zea mays), 3'ss of exon 1
lower sequence: EFJ35003 (Selaginella moellendorffii), 3'ss of exon 4
gtaccggacagtagttccttctgttgtcataccagtgttggggaaaaataaaacaaaacctaccacggtgccccccgcccgtaacgttgttgtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCCTCTACATGACGTACAGCGGCGAGAACACCTTCGGGCTGTTCTGAGTGGG-
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-------------------------------------gtatgagccgtcgagacgtaatc--ccacgtatattgatttacactattcctttccttttgtagCGGCATTGATATCGACCATCTACGAGGAGCACAAGGACGAGGATGGATTCCTCTACTTCACGTACAGCGGGGAGAATACCTTCGG-CCAAGAAGAACACTAMapped 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|84980803|gb|DW531152.1|DW531152EST: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAG CTGCTCTGATGTCTGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
genomic: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
EST:
gi|37391661|gb|CF633074.1|CF633074EST: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAG CTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
genomic: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataaaacaaaacctaccacggtgccccccgcccgtaacgttgttgtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCCTCTACATGACGTACAGCGGCGAGAACACCTTCGGGCTGTTCTGAGTGGG
ccgtaac putative branch site (score: 3)
ttgtccct putative PPT
aacaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccggacagtagttccttctgttgtcataccagtgttggggaaaaataaaacaaaacctaccacggtgccccccgcccgtaacgttgttgtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCCTCTACATGACGTACAGCGGCGAGAACACCTTCGGGCTGTTCTGAGTGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT