Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcaatcttcttcttcatggggcatgtatgcttcatcttctcaccaagtaatattagggataatttttatcaactgtcacgaaagattgaaccctgattgttgagtttttttcaacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGCTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGTACCCGC
Basic information
species | Glycine max |
transcript | GLYMA15G01510.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G01510.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 4
gtaagtcaatcttct-tcttcatggggcatgtatgcttcatcttctcaccaagtaatattagggataatttttatcaactgtcacgaaagattgaaccctgattgttgagtttttttcaacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGCTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGT-ACCCGC
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------aaagctactatcatcatagaagtactatg--tcatcattt-agaaaatactat----gaccagatgtatgagctaatgt-----attta--ccaagttttttaccaactttca---gAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGTTCAAATAGACGGTGTAAATAATAGTTCTACCACTGAAGATGGTCAACCA-
upper sequence: GLYMA15G01510.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 4
--------------gtaagtcaatc-ttcttcttcatggggca-tgtatgcttcatct-tctcaccaagtaatattagggataatttttatcaactgtcacgaaagattgaaccc----------------tgattgttgagttttttt---caacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGCTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGT-ACCCGC
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gtatgtgaagtcaagtttgctagttgttcatttactcgagtcaatgaaaatttcttcaatattttgcaccataagcatgaatgtatcattctgctggacaagaaaaaatgtacctatatcgccagttaatgtatttgtccattttttctacatatcagAGCATCTGGTGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGAAGATGGTCAGCCA-
upper sequence: GLYMA15G01510.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G017305_T02 (Zea mays), 3'ss of exon 1
-------------------------gtaagtca-atcttcttcttcatggggcatgt----atgcttcatcttctcaccaagta-atattag--ggataatttttatcaactgtcacgaaagattgaaccctgattgttgagtttttttc-----aacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGCTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGT-ACCCGC
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gtatgtggagttaattttcctagatgttgctcgtgtctacaagtcaatgaaaaattcctcaatattttgcactataagcaagaatgtatcattctgctagacaacagaaaatgtacctatatgtttaatg-tatttatccattttctttcttaatatcagTGCCTCCGGCGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGATGATGGCCAGCCA-
upper sequence: GLYMA15G01510.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtcaatcttcttcttcatggggcatgtatgcttcatcttctcaccaagtaatattagggataatttttatcaactgtcacgaaagattgaaccctgattgttgagtttttttcaacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGCTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGTACCCGC
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--------------------------------------gtaaattttcctgacgatactgag----atttcgat--actgaaatgaaaagt--atttgtaattggtggaggtgtgatg-cagGGGTTCTGGAGAGCATGAATCATCAAGAAGGGTGAAATCGGAACTCCTAGTTCAAGTAGATGGAGTGAGCAATACAGCGACAAATGAAGATGGTAGTCGCMapped 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|254319666|gb|GR830798.1|GR830798EST: CCAGTACAATTTTCATTGATGAAATTGATTCCTCTATGCAATGCTAGGGG GGCTCTCCTGGGGAGCATGAATCATCCAGAAGGGTGAAGTCTGAACTTCTA
genomic: CCAGTACAATTTTCATTGATGAAATTGATT-CTCTATGCAATGCTAGGGGgtaagtcaat ... ttttcaacagGGCT-T-CTGGGGAGCATGAATCATCCAGAAGGGTGAAGTCTGAACTTCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttatcaactgtcacgaaagattgaaccctgattgttgagtttttttcaacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGCTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGTACCCGC
ccctgat putative branch site (score: 4)
tttttttc putative PPT
tttttttcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcaatcttcttcttcatggggcatgtatgcttcatcttctcaccaagtaatattagggataatttttatcaactgtcacgaaagattgaaccctgattgttgagtttttttcaacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGCTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGTACCCGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG