Sequence
atgc intronic sequence ATGC exonic sequence...cttgagagtgaatcaggcctaattcatttctaatagactgattattttaacatttttttttcatttttgctttatgagcaactaatttgtatgtgctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCAAGGGGAATGGAAACTTGCTGTAGACATGATCCTTGATCCAAGAGATG
Basic information
species | Glycine max |
transcript | GLYMA03G40600.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G40600.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g43374.1 (Oryza sativa), 3'ss of exon 5
cttgagagtgaatcaggcctaattcatttctaatagactgattattttaacatttttttttcatttttgc--tttatgagcaactaatttgtatgtgctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCAAGGGGAATGGAAACTTGCTGTAGACATGATCCTTGATCCAAGAGATG
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---------gtatgaagccagaaccttttcgttatgcttcaaaacctaactggtacgtgtttacttttgaagctcatcaagttcatcttttttgttggttagCGTTTTGGAAGTGGTTCAGTACCTACTCACCTTGTTGGAGCTGCTTTGCTTAGAGGAGAGTGGAGAAGTTCTGTAAATTTGATTCTTGATCCAAGGGAAG
upper sequence: GLYMA03G40600.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G04820.1 (Arabidopsis thaliana), 3'ss of exon 9
-------------------------------------------------------cttgagagtgaatcaggccta-attcatttctaatag-actgatta---ttttaacatttttttttc--atttttgctttatgagcaactaatttgtatgtgctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCAAGGGGAATGGAAACTTGCTGTAGACATGATCCTTGATCCAAGAGATG
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gtactattctcttgtcgagttgtaatgatatatatgttattttctctttttagtttttagtagctaattcaacttacacttttgcattgtggtatcgagtagtacttgaatattatcaaatagaaatattttcttatgaattttgtaattgtgtg---acagCGTTTTGGAAGTGGTTCAGTACCAACCCACCATGTAGGAGCTGCACTATTGAAAGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAA
upper sequence: GLYMA03G40600.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 4
-----cttgagagtgaatcaggcctaattcatttctaatagactgattattttaacattttt--ttttcatttttgctttatgagcaactaatttgtatgtgctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCAAGGGGAATGGAAACTTGCTGTAGACATGATCCTTGATCCAAGAGATG
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gctttcttctgttacaccccatcccaccaaaaaaaaaaaaaaaggaaagcttcaaagtttatgattaccaaatttaactcattgg-aacaaattgctg------cagCGTTTTGGAAGTGGTTCTGTGCCAACTCACCTTATTGGAGCTGCATTACTCAGAGGAGAGTGGGAAACTGCTGTGAGCTTGATTCTGGATCCAAGAGAAGMapped 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|24205460|gb|BU964713.1|BU964713EST: CTGCAGATGCCTTAGGAAGGCACGGCTTCATTAACTACTTTGGTCTCCAG CGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTC
genomic: CTGCAGATGCCTTAGGAAGGCACGGCTTCATTAACTACTTTGGTCTCCAGgtaccttcta ... atgtgctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaacatttttttttcatttttgctttatgagcaactaatttgtatgtgctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCAAGGGGAATGGAAACTTGCTGTAGACATGATCCTTGATCCAAGAGATG
aactaat putative branch site (score: 2)
atttttttttcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgagagtgaatcaggcctaattcatttctaatagactgattattttaacatttttttttcatttttgctttatgagcaactaatttgtatgtgctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCAAGGGGAATGGAAACTTGCTGTAGACATGATCCTTGATCCAAGAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - tcaggcc