Sequence
atgc intronic sequence ATGC exonic sequence...taaaatgtctcactgagtacactgttttgtggtgtagatgatgcgtgtttgagtgttgcaagtgttgatgataagaatgggaacttatgtttgtttgcagGAGCCTGATTTGTTGCTGTTAGATGAGCCTACAAATCACCTTGATCTTGACACCATTGAGTGGCTTGAAGACTATCTTAACCAGCAGGATGTTCCAATGG
Basic information
species | Glycine max |
transcript | GLYMA04G39670.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G39670.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g39020.1 (Oryza sativa), 3'ss of exon 1
--------------------------------------------------------------------------------taaaatgtctcactgagtaca---ctgttttgtggtgtagatgatgcgtgtttgagtgttgcaagtgttgatgataagaatgggaacttatgtttgtttgcagGAGCCTGATTTGTTGCTGTTAGATGAGCCTACAAATCACCTTGATCTTGACACCATTGAGTGGCTTGAAGACTATCTTAACCAGCAGGATGTTCCAATGG
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gtacagataaaaaagaaaatttgagctctacatgtagcaatcaatggttgtcatattgtgatggagagaaaaatgagtggtattatggccaattggtgatgaatttggtctggattgttgaatttgaattgtagtttttagtgtctgtgtgcatttccaatgctgaaat-tgattgtgtgcagGATCCCGATTTGCTGCTGCTCGATGAGCCGACCAATCACGTCGATTTGGACACCATTGAGTGGCTGGAGAGTTACCTCAAGACGCAGGAAGTGCCGATGG
upper sequence: GLYMA04G39670.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G64840.1 (Arabidopsis thaliana), 3'ss of exon 1
taaaatgtctcactgagtac--actgttttgtggtgtagatgatgcgtgtttgagtgttgcaagtgttgatgataagaatgggaacttatgtttgtttgcagGAGCCTGATTTGTTGCTGTTAGATGAGCCTACAAATCACCTTGATCTTGACACCATTGAGTGGCTTGAAGACTATCTTAACCAGCAGGATGTTCCAATGG
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gtatatgaatgattgtttacttaaagttttatcctttcaatga-----gtttgaactc----aaagctaatgtgaatgaattgtgtgtttctttgcgagtagGATCCAGATTTGCTGCTACTTGATGAGCCGACAAATCATTTGGATCTTGATACTATTGAGTGGCTTGAAGGTTATTTGCAAAAGCAAGATGTGCCTATGG
upper sequence: GLYMA04G39670.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0031g01640.t01 (Vitis vinifera), 3'ss of exon 1
-taaaatgtctcactgagtacactgttttgtggtgtagatgatgcgtgtttgagtgttgcaagtgttgatgataagaatggga---acttatgtttgtttgcagGAGCCTGATTTGTTGCTGTTAGATGAGCCTACAAATCACCTTGATCTTGACACCATTGAGTGGCTTGAAGACTATCTTAACCAGCAGGATGTTCCAATGG
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ttaaaatgtttaagt---tttgttagccttttatatttataatttgtactagaatgc-gtggttgttattgatcggttataaatatacttgtgatcacttgcagGAGCCAGATTTATTACTATTGGATGAGCCCACAAATCACCTTGATCTTGACACAATTGAATGGCTTGAAGGTTATCTTAACAAGCAGGATGTGCCCATGGMapped 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|254327296|gb|GR836905.1|GR836905EST: TCAGTGGAGGCTGGCAGATGAGGATGTGTCTCGGCAAGATTCTACTTCAG GAGCCTGATTTGTTGCTGTTAGATGAGCCTACAAATCACCTTGATCTTGAC
genomic: TCAGTGGAGGCTGGCAGATGAGGATGTGTCTCGGCAAGATTCTACTTCAGgtgtgttaat ... ttgtttgcagGAGCCTGATTTGTTGCTGTTAGATGAGCCTACAAATCACCTTGATCTTGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttgagtgttgcaagtgttgatgataagaatgggaacttatgtttgtttgcagGAGCCTGATTTGTTGCTGTTAGATGAGCCTACAAATCACCTTGATCTTGACACCATTGAGTGGCTTGAAGACTATCTTAACCAGCAGGATGTTCCAATGG
tgttgat putative branch site (score: 4)
tttgttt putative PPT
ataagaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaaatgtctcactgagtacactgttttgtggtgtagatgatgcgtgtttgagtgttgcaagtgttgatgataagaatgggaacttatgtttgtttgcagGAGCCTGATTTGTTGCTGTTAGATGAGCCTACAAATCACCTTGATCTTGACACCATTGAGTGGCTTGAAGACTATCTTAACCAGCAGGATGTTCCAATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - ctcactg
- - - - - - - - - - - - - -tgtggtg
- - - - - - - - - - - - - - - - - - - - -tgcgtgt
- - - - - - - - - - - - - - - - - - - - - - - - -tgagtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgatg