Sequence
atgc intronic sequence ATGC exonic sequencegtatgcccccttcaattataataaaagtacatgatatataaattggtgattgttattttcttcaattgtcgggacatataagctatgttctgagtttaaattctaaatattcataatttcatataattatattttgttttcagGTGATCTCAAGCGTATTTGTGAAACGGACCTTGGTTTAATTTCTCAATGTTGTTTGACTAAGCATGTCTTTAAGATCACTAAGCAGTATTTGGCTAATGT
Basic information
species | Glycine max |
transcript | GLYMA10G00530.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 12
gtatgcccccttcaattataataaaagtacatgatatataaattggtgattgttattt-tcttcaattgtcgggacatataagctatgttctgagtttaaattctaaatattcataatttcatataattatattttgttttcagGTGATCTCAAGCGTATTTGTGAAACGGACCTTGGTTTAATTTCTCAATGTTGTTTGACTAAGCATGTCTTTAAGATCACTAAGCAGTATTTGGCTAATGT
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--------------------------gtaagtgccat-----ctgctaattgctttgaatatataattacttcaactcttaca-tattttatcagatataactttatatatatttaaagcgatataacttcat---atgtgtagGTGACATCAAACGTATTTGTGAAACTGATTTGGGGTTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAGCAGTACTTGGCAAATGT
upper sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 12
gtatgcccccttcaattataataaaagtacatgatatataaattggtgattgttattttcttcaattgtcgggacatataagctatgttctgagtttaaattctaaatattcataatttcatataattatattttgt--tttcagGTGATCTCAAGCGTATTTGTGAAACGGACCTTGGTTTAATTTCTCAATGTTGTTTGACTAAGCATGTCTTTAAGATCACTAAGCAGTATTTGGCTAATGT
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------------------------------------------------------gtattatttcgacatccataaacttaacccttttgccttctttagt-----aatggttttgatgaaaacgaaatgtttcttgtaatctcagGTGATCTTAAGAGAATCTGTGAAACCGAGCTTGGTTTGATATCTCAATGTTGTCTCACAAAACATGTGTTCAAGATTAGCAAACAGTATCTGGCAAATGT
upper sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 10
------------gtatgcccccttcaattataataaaagtacatgatatataaattggtgattgttattttcttcaattgtcgggacatataagctatgttctgagtttaaattctaaatattcataatttcatataattatattttgttttcagGTGATCTCAAGCGTATTTGTGAAACGGACCTTGGTTTAATTTCTCAATGTTGTTTGACTAAGCATGTCTTTAAGATCACTAAGCAGTATTTGGCTAATGT
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gtatgttaaggttcttgtttctatcaaacagattaaaactctttcatttaagtcctgacgacttatgggtaatgttaactttggcataatctggttggacttttatttgcgattttatttaagcttgattctatcta-ttgtgcatggtatgtagGTGATCTGAAGAAGCAATGTGAGACTGTCCTGGGAGTGGTTTCACAATGTTGTTTGACTAAGCATGTCTTCAAGATGAGCAAGCAGTATTTAGCAAATGTMapped 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|18041185|gb|BM309479.1|BM309479EST: ATTGGAGCTTTTGTTAGCAATATTGCCCGACAACAATGGTTCTCTCTATG GTGATCTCAAGCGTATTTGTGAAACGGACCTTGGGTTAATTTCTCAATGTT
genomic: ATTGGAGCTTTTGTTAGCAATATTGCCCGACAACAATGGTTCTCTCTATGgtatgccccc ... ttgttttcagGTGATCTCAAGCGTATTTGTGAAACGGACCTTGGTTTAATTTCTCAATGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgagtttaaattctaaatattcataatttcatataattatattttgttttcagGTGATCTCAAGCGTATTTGTGAAACGGACCTTGGTTTAATTTCTCAATGTTGTTTGACTAAGCATGTCTTTAAGATCACTAAGCAGTATTTGGCTAATGT
ttctaaa putative branch site (score: 2)
ttttgttttc putative PPT
tttaaattctaaatat 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
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gtatgcccccttcaattataataaaagtacatgatatataaattggtgattgttattttcttcaattgtcgggacatataagctatgttctgagtttaaattctaaatattcataatttcatataattatattttgttttcagGTGATCTCAAGCGTATTTGTGAAACGGACCTTGGTTTAATTTCTCAATGTTGTTTGACTAAGCATGTCTTTAAGATCACTAAGCAGTATTTGGCTAATGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA