Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttggaaatggataaataattttctatattttttagttgacagtttctgcataatttctttcatgcttgtccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG
Basic information
species | Glycine max |
transcript | GLYMA04G40420.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G40420.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g06200.1 (Oryza sativa), 3'ss of exon 4
gtaagttttggaaatggataaataattttctatattttttagttgacagtttctgcataatttctttcatgcttgtccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG
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gtatgcctttttgcttctgaattgttgagctataactgtttcctgtaacatttctgatg-----tttaataattgac--tatgcagGGGATATATCTCCGCCACGTGGTGTTAAGGTGGCTATGGAGATGCAAGCAGAAGCAGAAAGGAAAAAGCGTGCCCAAATCCTTGAATCAGAAG
upper sequence: GLYMA04G40420.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G023073_T01 (Zea mays), 3'ss of exon 4
gtaagtt-ttggaaatggataaataattttctatattttttagttgacagtttctgcataatttctttcatgcttgtccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG-------
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gtatgccgtcttttcctgtttgagcattagagctataatacacgcattgtttcaaatgtcaatgttttaa-atttgacaat--gcagGGGACATAAATCCTCCAGCAGGGATTAGGCAGGCTATGGAGATGCAGGCTGAGGCAGAAAGGAAAAAACGCGCTCAAATCCTTGAGTCAGAAGGGATGAA
upper sequence: GLYMA04G40420.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G27585.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagttttggaaatggataaataattttctatattttttagttgacagtttctgcataatttctttcatgcttgtccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG
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gtaagttgttcgtgttttt---tcttttccggtgatagttacatatctgttttttccta---tttctaattcatgtttttc--cagGGGATATTATGCCCCCTCATGGAGTGCGAGCTGCTATGGAAATGCAAGCTGAAGCTGAGCGTAAAAAGAGAGCCCAGATTCTTGAGTCTGAAG
upper sequence: GLYMA04G40420.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G54100.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagttttggaaatggataaataattttctatattttttagttgacagtttctgcataatttctttcatgcttgtccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG
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gtgagttatttttctgt-tgactctttgctggtgttagctagat-acccttttggccttgtatcta--atacatgtatatc--cagGGGATATCATGCCTCCTAATGGAGTGAGAGTTGCTATGGAAATGCAAGCTGAAGCTGAACGTAAAAAGAGAGCCCAGATTCTTGAGTCTGAAG
upper sequence: GLYMA04G40420.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g01630.t01 (Vitis vinifera), 3'ss of exon 4
----gtaagtttt-----ggaaatggataaataattttctatattttttagttgacagtttctgcataatttctttcatgcttgtcctt-ctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG
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gtaggtgaccttttatctaaatatttcttatggactttctttgctatatcacccatagcagcattcctatatgcctcattgtcctcttttctttagGGGATATATCTCCTCCTCGTGGAGTGAGGGCAGCTATGGAGATGCAAGCAGAAGCAGAACGTAAAAAGAGAGCTCAAATTCTTGAATCAGAGGMapped 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|192300517|gb|FG991499.1|FG991499EST: TAATATGGCTGCAAAAAGTTGGGGTCTGGAGTGCCTTCGATATGAAATAA GGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAG
genomic: TAATATGGCTGCAAAAAGTTGGGGTCTGGAGTGCCTTCGATATGAAATAAgtaagttttg ... ccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAG
EST:
gi|151395353|gb|EV265224.1|EV265224EST: TAATATGGCTGCAAAAAGTTGGGGTCTGGAGTGCCTTCGATATGAAATAA GGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAG
genomic: TAATATGGCTGCAAAAAGTTGGGGTCTGGAGTGCCTTCGATATGAAATAAgtaagttttg ... ccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattttttagttgacagtttctgcataatttctttcatgcttgtccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG
agttgac putative branch site (score: 4)
tttctttcatgcttgt putative PPT
ataatttctttcat 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 |
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gtaagttttggaaatggataaataattttctatattttttagttgacagtttctgcataatttctttcatgcttgtccttctgtagGGGATATCTCTCCTCCACGTGGAGTGAGAGCAGCTATGGAGATGCAAGCAGAAGCAGAAAGAAAAAAGAGAGCTCAAATTCTTGAGTCTGAAG
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