Sequence
atgc intronic sequence ATGC exonic sequencegtaatttgttctttctcaagtatctatgtcattactacttttcatcttctatggatgataattatcttctgatttcctaccactatttttctgcagATACGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTATATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
Basic information
species | Glycine max |
transcript | GLYMA11G12570.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G12570.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G34500.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaatttgttctttctcaagtatctatgtcattactacttttcatcttc-tatggatgataattatcttctgatttcctaccactattt----ttctgcagATACGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTATATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
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-------gtatatatatagataccctctcttctttcagttatcaggctcatattgtt--tctttacattttatcttcttacacctttttaactttctgcagATATGTTTCACCGGAATATGCAAGTACTGGTATGCTCAATGAGTGTAGTGATGTCTACAGTTTCGGTGTTCTGCTCATGGAGATCATTACAGGAAGGAGC
upper sequence: GLYMA11G12570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0063g02510.t01 (Vitis vinifera), 3'ss of exon 4
-----------------gtaatttgttctttctcaagtatctat--gtca--ttactactt---ttcatcttctatggatg-ataattatcttctgatttcctaccactatttttctgcagATACGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTATATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
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gtatgttcttcctcggtttcctataatatttttcaataatttgttagttagatttaaacttgaatgtattatttctctgtacacatgtattattaagttatttatcatcatttttctgtagATATGTCTCTCCCGAGTATGCAAGCACGGGTATGCTTAGTGAAGGGAGTGATGTCTATAGTTTTGGAGTTCTACTTATGGAGATAATTACTGGAAGGAGC
upper sequence: GLYMA11G12570.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------gtaatttgttctttctc---aagtatctatgtcattactacttttca-------tcttctatggatgataattatcttct-gatttcctaccactatt-tttctgcagATACGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTATATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
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gtaagcgtaaagtatgatttattgcctcgttgtaacaataattgcagctagcaacggtgacaagtatttgtttgtctttcatggttttctccttgagtcgttacgatggttgtttttgcagGTATGTAGCCCCCGAGTACGCGAACACGGGCCTGCTGAACGAGCGAAGTGATGTGTACAGCTTTGGGGTGCTTCTCATGGAGATTATCACCGGGCGAGAT
upper sequence: GLYMA11G12570.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------gtaatttgttctttctcaagtatcta-tgtc-attactacttttcatct---tctatgg---atgataattatcttctgatttcctaccactatttttctgc----------agATACGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTATATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
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gtaagctcaaggccctcctctggattgtattgtattgttgaaacagtagttgcagttataaacggcatttaatgtcgatttcttctagtcacatagttttatgtcgcgtgtttctcaacgttctagtccccatccccattctttggctgtatcactcagGTACGTAGCGCCGGAGTACGCGAACACGGGCCTGCTGAATGAGCGAAGCGATGTGTACAGCTTTGGGGTGCTTCTCATGGAGATCATCACGGGGCGAGAT
upper sequence: GLYMA11G12570.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 5
gtaatttgttctttctcaagtatctatgtcattactacttttcatcttctatggatgataattatcttctgatttcctaccactatttttctgcagATACGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTATATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
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----------------------------gtatgagaa--ttcaatcctctttgctcgcgaacgatca---aagtttttgtt----ctttgtcgcagCTATGTCGCTCCAGAGTACGCTAACACTGGTCTACTCAACGAGAGAAGCGACGTTTATAGCTTTGGAGTTCTTCTCATGGAGATGATCACTGGGAGAGATMapped 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|18730107|gb|BM525686.1|BM525686EST: TTAGGATCTGAGAAAACACACGTGACTACGCGTGTAATGGGAACATTTGG ATACGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGA
genomic: TTAGGATCTGAGAAAACACACGTGACTACGCGTGTAATGGGAACATTTGGgtaatttgtt ... ttttctgcagATACGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatcttctatggatgataattatcttctgatttcctaccactatttttctgcagATACGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTATATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
ttctgat putative branch site (score: 3)
ctatttttct putative PPT
atgataattatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttgttctttctcaagtatctatgtcattactacttttcatcttctatggatgataattatcttctgatttcctaccactatttttctgcagATACGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTATATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC