Sequence
atgc intronic sequence ATGC exonic sequence...ggtatcttcattttaaggtttgtgttattatgctgttctagtgataggtaaaagttctcaagttatatctgactgcatgagctatctggtacatttgtagGTATCCTTATATGGCAGTGGTTCTAAATTTCAGTCAGTCATGGGCTTTGTACTGCCTTGTTCAATTTTATACAGTTACAAAGGACGAACTGGCTCATATA
Basic information
species | Glycine max |
transcript | GLYMA04G00250.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G00250.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G088737_T01 (Zea mays), 3'ss of exon 6
ggtatctt-cattttaaggtttgtgttattatgctgttctagtgataggtaaaagttctcaagttatatctgactgcatgagctatctggtacatttgtagGTATCCTTATATGGCAGTGGTTCTAAATTTCAGTCAGTCATGGGCTTTGTACTGCCTTGTTCAATTTTATACAGTTACAAAGGACGAACTGGCTCATATA
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attatgttgcagcgcactgtgaacttgctcatgcatttgatgacataggaattaaacaatcgttgtcttcccattac-tgaagtatttacttgcctaccagGTACTCTTACACGGCTGTGGTTCTCAATTTCAGTCAGTCATGGGCCTTATACTGTCTCGTTCAGTTCTATGCTGTGATAAAGGATGAGTTAGCTCATATA
upper sequence: GLYMA04G00250.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G373717_T01 (Zea mays), 3'ss of exon 5
------------------------ggtatcttcattttaaggtttgtgttattatgctgttctagtgataggta---aaagttctcaagttatatctgactgca--tgagctatctggtacatttgtagGTATCCTTATATGGCAGTGGTTCTAAATTTCAGTCAGTCATGGGCTTTGTACTGCCTTGTTCAATTTTATACAGTTACAAAGGACGAACTGGCTCATATA
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gtaagaggcatatactttttttttgttttgcacatgtgctagctctggtcaacttgctcatgcatttgatggcataggaaatgaacaatcattgccttgccattactgaactatttacttatctaccagGTACTCTTACACGGCCGTGGTTCTCAATTTCAGTCAGTCATGGGCCTTATACTGTCTCGTCCAGTTCTACACCGTGATAAAGGATGAGTTAGCTCATATA
upper sequence: GLYMA04G00250.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G38360.2 (Arabidopsis thaliana), 3'ss of exon 5
-------ggtatcttcattttaaggtttgtgttattatgctgttctag--tgataggtaaaagtt--ctcaagttatatctgactgca--tgagctatctgg----taca------------tttgtagGTATCCTTATATGGCAGTGGTTCTAAATTTCAGTCAGTCATGGGCTTTGTACTGCCTTGTTCAATTTTATACAGTTACAAAGGACGAACTGGCTCATATA
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gtacgttgagacaattttgacaagaacagtgctaacatacagattgaccttaagaaacgaaaatcagtttcatctatgatggactgtgatcaagatagcagcatcttaccattgttttcttttttgtagGTACCCTTATTTGGCAGTTGTTCTAAATTTTAGTCAGTCATGGGCATTATACTGTCTGGTTCAGTTCTATGGTGCAACGAAAGATGAGCTTGCACACATC
upper sequence: GLYMA04G00250.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g03670.t01 (Vitis vinifera), 3'ss of exon 6
ggtatcttcattttaaggtttgtgttattatgctgttctagtgataggtaaaagttctcaagttatatctgactgcatgagctatctggtacatttgtagGTATCCTTATATGGCAGTGGTTCTAAATTTCAGTCAGTCATGGGCTTTGTACTGCCTTGTTCAATTTTATACAGTTACAAAGGACGAACTGGCTCATATA
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-gtaagatagtttggaaataattgttggaaaattttt----tgctaacttgatttgtttaaat-gtctcttacagttgtagacttctgtt---tttgtagGTATCCTTACATAGCAGTGGTTCTAAATTTCAGTCAATCATGGGCTCTGTACTGCTTAGTTCAGTTTTATACTGTTACAAAGGATGAATTGGAGCACATAMapped 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|21887467|gb|BQ740680.1|BQ740680EST: CTTGAAGCCTTTGGAGTCTACTGTGAAGGAGAATTTAAAGTAGGATGTGG GTATCCTTATATGGCAGTGGTTCTAAATTTCAGTCAGTCATGGGCTTTGTA
genomic: CTTGAAGCCTTTGGAGTCTACTGTGAAGGAGAATTTAAAGTAGGATGTGGgtaagaaatt ... acatttgtagGTATCCTTATATGGCAGTGGTTCTAAATTTCAGTCAGTCATGGGCTTTGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggtaaaagttctcaagttatatctgactgcatgagctatctggtacatttgtagGTATCCTTATATGGCAGTGGTTCTAAATTTCAGTCAGTCATGGGCTTTGTACTGCCTTGTTCAATTTTATACAGTTACAAAGGACGAACTGGCTCATATA
atctgac putative branch site (score: 3)
aagttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtatcttcattttaaggtttgtgttattatgctgttctagtgataggtaaaagttctcaagttatatctgactgcatgagctatctggtacatttgtagGTATCCTTATATGGCAGTGGTTCTAAATTTCAGTCAGTCATGGGCTTTGTACTGCCTTGTTCAATTTTATACAGTTACAAAGGACGAACTGGCTCATATA
- - -cttcatt
- - - - - - - - -gtttgtg
- - - - - - - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatctg