Sequence
atgc intronic sequence ATGC exonic sequence...atataatattgagcgggtgttttcactttccgtggaatatatatattttgggtagcattgctttgtgtactaaattttagttgtttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
Basic information
species | Glycine max |
transcript | GLYMA11G03800.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G03800.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 3
ata-taatattgagcg-ggtgttttcactttccg-tggaatatatatattttgggtagcattgctttgtgtactaaatt--ttagttg--------------ttt-------atattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
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gtactaatatcgaccatattatcttcactatctactccaatatacagcactgaagctgctcaattttatccacaagctcgattaattaatagggaacaatactttgtgcaaaattttattttgcagGGCATGTTTGTTCCTGCTATAAAAGGCCAAGGGACTGAAGAGCAGCAGAAGAAGTGGCTACCTCTGGCCTACAGGTTCCAAATAATTGGATGCTATGCTC
upper sequence: GLYMA11G03800.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 3
atataatattgagcgggtgttttcactttccgtggaatatatatattttgggtagcattgctttgtgtactaaattttagttgtttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
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aacagatataagattcctgccattgaataacatatagtttttgtacaagcttcatcaatattttcaccttacaagttacaaaaacaatgtcatcttgcagGGCATGTTTGTTCCTGCTATAAAAGGTCAAGGTACTGAGGAGCAGCAGAAAAAGTGGTTACCAATGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC
upper sequence: GLYMA11G03800.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G052389_T01 (Zea mays), 3'ss of exon 3
-atataatattga-gcgggtgttttcactttccgtggaatatatatattttgggtagcattgctttgtgtactaaattttagttgtttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
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catagaagattcataccacggaaggaacaccagatagttgctttgtacaagctttatcttctttttgttaactta-ttacagacaca-atacgatcttgcagGGCATGTTCGTTCCAGCTATAAAAGGCCAAGGAACTGAGGAGCAGCAGCACAAGTGGTTACCACTGGCTTACAAGTTCCAAATAATTGGGTGCTATGCTC
upper sequence: GLYMA11G03800.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G35690.1 (Arabidopsis thaliana), 3'ss of exon 2
atataatattgagcgggtgttttcactttccgtggaatatatatatt---ttgggtagcattgctttgtgtactaaattttagttgtttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
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------------------------gtataacacaaaatttacaatttcccttgggtggt-ttaattagaattttggtgttgaattggttttgtggtgg-atagGGAATGTTTGTGCCTGCAATTAAAGGACAAGGCACAGAGCAACAACAACAAAAGTGGTTGTCTTTAGCTACTAAGATGCAGATAATTGGATGTTATGCTCMapped 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|192300456|gb|FG988843.1|FG988843EST: ATAAGCTCAGATCTTTTGTGGATCAACCTGCATTTACGGATCTTCATTGG GGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAG
genomic: ATAAGCTCAGATCTTTTGTGGATCAACCTGCATTTACGGATCTTCATTGGgtataattca ... tcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgggtagcattgctttgtgtactaaattttagttgtttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
tactaaa putative branch site (score: 1)
tattctttt putative PPT
tactaaattttagttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atataatattgagcgggtgttttcactttccgtggaatatatatattttgggtagcattgctttgtgtactaaattttagttgtttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - gggtgtt
- - - - - - - - - - - - - -ttccgtg