Sequence
atgc intronic sequence ATGC exonic sequence...tttgctaaatcaggcccatgtttttcttcagtgctcctcatgctggcttgtatgttttcatttatccaaataatagattcttttggaattggatctgtagGGAGATGAAGAAGTTGGGGTTGCCCTTTTGACTTATCCTGTTCTGATGGCTTCTGATATACTTCTATATCAG
Basic information
species | Glycine max |
transcript | GLYMA04G09130.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G09130.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g54020.2 (Oryza sativa), 3'ss of exon 6
tttgctaaa---tcaggcccatgtttttcttcagtgctcctcatgctggcttgtatgttttcatttatccaaataatagattcttttggaattggatctgtagGGAGATGAAGAAGTTGGGGTTGCCCTTTTGACTTATCCTGTTCTGATGGCTTCTGATATACTTCTATATCAG
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---gcaaaaccctcaactccttatatcatggtgttgtactgtttaatccgtcctattttggcaaatttttattttgttgggtttatttttttcttatttatagGGTGATGAAAATGTTGGAGTGGCACTTTTGACTTATCCTGTTTTAATGGCTTCTGACATTCTCCTGTACCAG
upper sequence: GLYMA04G09130.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G177970_T02 (Zea mays), 3'ss of exon 6
tttgctaaatcaggcccatgtttttcttcagtgctcctcatgctggcttgtatgttttcatttatccaa--------ataatagattcttttggaattggatctgtagGGAGATGAAGAAGTTGGGGTTGCCCTTTTGACTTATCCTGTTCTGATGGCTTCTGATATACTTCTATATCAG
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----agagtccattgttgcagaatccttcaatgc--cttatggtg--ttacatatttcagattgctgaaggttgactataatagtactgttgatgatttttttaatagGGTGATGAAAATGTTGGGGTTGCACTTTTGACTTATCCTGTTCTAATGGCTTCTGACATTCTTTTGTACCAG
upper sequence: GLYMA04G09130.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0008g00200.t01 (Vitis vinifera), 3'ss of exon 6
tttgctaaatcaggcccatgtttttcttcagtgctcctcatgctggc----ttgtatgttttcatttatccaaataatagattcttttggaattg-gatctgtagGGAGATGAAGAAGTTGGGGTTGCCCTTTTGACTTATCCTGTTCTGATGGCTTCTGATATACTTCTATATCAG
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-----tattttgcacttgtaatgttcaatcatggtttgagaatgagcattcttctaacttttccagtgccattacacaagatgttcttcaatttctgttttgtagGGAGATGAAAATGTTGGGGTTGCCCTTCTGACTTATCCTGTTCTCATGGCTTCTGATATTCTTTTATATCAGMapped 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|23063730|gb|BU578612.1|BU578612EST: TTGGGTGGCTGAACAAAATGATACAGTTTAAAGAGAAATCTCGCAAGGCG GGAGATGAAGAAGTTGGGGTTGCCCTTTTGACTTATCCTGTTCTGATGGCT
genomic: TTGGTTGGCTGAACAAAATGATACAGTTTAAAGAGAAATCTCGCAAGGCGgtgcgttcat ... ggatctgtagGGAGATGAAGAAGTTGGGGTTGCCCTTTTGACTTATCCTGTTCTGATGGCT
EST:
gi|6482637|gb|AW201882.1|AW201882EST: TTGGTTGGCTGAACAAAATGATACAGTTTAAAGAGAAATCTCGCAAGGCG GGAGATGAAGAAGTTGGGGTTGCCCT
genomic: TTGGTTGGCTGAACAAAATGATACAGTTTAAAGAGAAATCTCGCAAGGCGgtgcgttcat ... ggatctgtagGGAGATGAAGAAGTTGGGGTTGCCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttgtatgttttcatttatccaaataatagattcttttggaattggatctgtagGGAGATGAAGAAGTTGGGGTTGCCCTTTTGACTTATCCTGTTCTGATGGCTTCTGATATACTTCTATATCAG
ttttcatttatccaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgctaaatcaggcccatgtttttcttcagtgctcctcatgctggcttgtatgttttcatttatccaaataatagattcttttggaattggatctgtagGGAGATGAAGAAGTTGGGGTTGCCCTTTTGACTTATCCTGTTCTGATGGCTTCTGATATACTTCTATATCAG
- - - - - caggccc
- - - - - - - - - - - - - -tcagtgc
- - - - - - - - - - - - - - - - - - -tcatgct
- - - - - - - - - - - - - - - - - - - - - - -gcttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttttgg