Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcttcccttcctaaactgtttgtattagacagtcaatttatactatactacttgttgaggtataatcataagcttgaactccatcaactttcctttttaagtctctgattcatgttctatgcaccctttagCGTGAGTTCTATCTTGAAGGAGGGGCCATGGTCTTGGCTGACGGAGGTGTTGTCTGCATTGATGAGTTTGATAAGATGAGGCCAGAAGATAG
Basic information
species | Glycine max |
transcript | GLYMA13G22420.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 10
gtaagttcttcccttcctaaactgtttgtattagacagtcaatttatactatactacttgttgaggtataatcataagcttgaactccatcaactttcctttttaagtctctgattcatgttctatgcaccctttagCGTGAGTTCTATCTTGAAGGAGGGGCCATGGTCTTGGCTGACGGAGGTGTTGTCTGCATTGATGAGTTTGATAAGATGAGGCCAGAAGATAG
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------------------------------------------gtaagcttgtcttccctgc--aaggattattgt--gttt--actcaaagttctgtttcctagaactaaaagacttattttccctgtac-----agCGAGAGTTTTATTTGGAAGGAGGGGCCATGGTTTTGGCTGATGGTGGAGTTGTTTGTATTGATGAGTTTGACAAAATGAGGCCTGAGGACCG
upper sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaagttcttcccttcctaaactgtttgtattagacagtcaatttatactatactacttgttgaggtataatcataagcttgaactccatcaactttcctttttaagtctctgattcatgttctatgcacccttt--agCGTGAGTTCTATCTTGAAGGAGGGGCCATGGTCTTGGCTGACGGAGGTGTTGTCTGCATTGATGAGTTTGATAAGATGAGGCCAGAAGATAG
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------------------------------------------------gtatgtcctatcttcaagtgtttttctatgatttgtttaaaagtagttgctatgacagattctcagttatttatacatatgttcattgcagCGAGAGTTCTATCTTGAAGGTGGTGCTATGGTTTTGGCTGATGGAGGTGTTGTGTGTATTGATGAATTTGACAAGATGAGACCGGAAGATAG
upper sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 9
gtaagttcttcccttcctaaactgtttgtattagaca----gtcaatt-tatactatactacttgttgaggta----taatcat--aagct--tgaactccatcaactttccttt------ttaagtc-tctga-ttcatgttcta----tgcaccctttagCGTGAGTTCTATCTTGAAGGAGGGGCCATGGTCTTGGCTGACGGAGGTGTTGTCTGCATTGATGAGTTTGATAAGATGAGGCCAGAAGATAG
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gtaagtttttgagattctctatcatgtgtgctgatcctaatgtcaattctctagctctttctttctccagataagctttgtcaatggagccgatgagtttatttaaattccctcaaaataattaggttatctgacttcaaattcaaactctacatgattcagCGTGAATTTTATCTAGAAGGAGGAGCAATGGTTTTGGCAGATGGAGGTGTTGTCTGTATTGATGAGTTTGACAAAATGAGGGCAGAGGACAG
upper sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S355_49V6.1 (Physcomitrella patens), 3'ss of exon 10
----------gtaagttcttcccttcctaaactgtttgtattagacagtcaatttatactatactacttgttgaggtataatcata--agcttgaactccatcaacttt---cctttttaagtctctga---ttcatgttc-tatgcaccctt-----------tagCGTGAGTTCTATCTTGAAGGAGGGGCCATGGTCTTGGCTGACGGAGGTGTTGTCTGCATTGATGAGTTTGATAAGATGAGGCCAGAAGATAG
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gtatgcaattttacatttgccccgtgtttttatctttctaccaaactctcacctgagcatgttttgcttactgaacgtttctcgtttcacatagcaaaccatctatggcaagtgttttgaaatatcgaaatgttaatagtcgcttacacctgtgtcctaaatcacagAGAGAGTTTTACCTTGAAGGAGGTGCTATGGTTCTTGCTGATGGAGGTGTTGTCTGCATTGATGAGTTCGACAAAATGCGACCTGAAGACAGMapped 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|207814654|gb|GD788563.1|GD788563EST: GCTCATCAGCGGCTGGCCTGACCGCTTCTGTAATCCAAGATAGTGGCACT CGTGAGTTCTATCTTGAAGGAGGGGCCATGGTCTTGGCTGACGGAGGTGTT
genomic: GCTCATCAGCGGCTGGCCTGACCGCTTCTGTAATCCAAGATAGTGGCACTgtaagttctt ... caccctttagCGTGAGTTCTATCTTGAAGGAGGGGCCATGGTCTTGGCTGACGGAGGTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactccatcaactttcctttttaagtctctgattcatgttctatgcaccctttagCGTGAGTTCTATCTTGAAGGAGGGGCCATGGTCTTGGCTGACGGAGGTGTTGTCTGCATTGATGAGTTTGATAAGATGAGGCCAGAAGATAG
ctctgat putative branch site (score: 4)
cacccttt putative PPT
tttttaagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcttcccttcctaaactgtttgtattagacagtcaatttatactatactacttgttgaggtataatcataagcttgaactccatcaactttcctttttaagtctctgattcatgttctatgcaccctttagCGTGAGTTCTATCTTGAAGGAGGGGCCATGGTCTTGGCTGACGGAGGTGTTGTCTGCATTGATGAGTTTGATAAGATGAGGCCAGAAGATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG