Sequence
atgc intronic sequence ATGC exonic sequence...ctaagatgcattctctctgatctgcatataatttacttgtctagatcatttgatgatttgaaaaattcatttggttttctgttggtccattgtattaaagTTGTTGGAGACAATCATAAAGAACTGTGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG
Basic information
species | Glycine max |
transcript | GLYMA17G26440.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 2
ctaagatgcattctctctgatctgcatataatttacttgtctagatca-tttg---atgatttgaaa--aat--tcatttggttttctgttggtccattgtattaaagTTGTTGGAGACAATCATAAAGAACTGTGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG
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------tgcttcattattattttggagatgtat--cttgtttaggacaacttgcacaggatctaaaatgaataatatcctgattttttttgggggagctctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG
upper sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g17350.1 (Oryza sativa), 3'ss of exon 3
-ctaagatgcattctctctgatctgcatataatttacttgtctagatcatttgatgatttgaaaaattcatttggttttctgttggtccattgtattaaa----gTTGTTGGAGACAATCATAAAGAACTGTGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG
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tttgaaatgtcctgttcctcacc-----atgcttgaaaagttgaaacggaaagccacatctaagtaatcctttactgaactgcaacctttctctgcttgattcagTTACTGGAGACGATGATCAAAAACTGTGGGGACATTGTCCATATGCAAGTTGCTGAGAAAGACATACTTCATGAAATGGTGAAAATAGTCAAGAAAAGG
upper sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G153138_T02 (Zea mays), 3'ss of exon 2
-ctaagatgcattctctctgatctgcatataatttacttgtctagatcatttgatgatttgaaaaattcatttggttttctgttggt-ccattgtattaaagTTGTTGGAGACAATCATAAAGAACTGTGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG
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cataacttgtatttaataaggttt-tatatgatg-attattctctatttcgttattatgaaaatattagcattgtctttcagatgacatctctctatttcagTTGTTGGAAACTGTTATTAAAAACTGTGGGGATATACTTCACATGCATGTCGCAGAGAGAGATATATTGCATGAGATGGTGAAGATAGTGAAGAAAAAG
upper sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G062953_T01 (Zea mays), 3'ss of exon 2
ctaagatgcattctctctgatctgcatataatt-tacttgtctagatcatttgatgatt--tgaaaaattcat-ttggttttctgttggt-ccattgtattaaagTTGTTGGAGACAATCATAAAGAACTGTGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG
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-----gtagaacatgtataattttgttatgatgatttttaaatttaatatttagctattgccaaaatgttagcattgtcttgctgatgatatctctatatttcagCTGTTGGAAACTGTTATAAAAAATTGTGGGGATATACTTCACATGCATGTTGCAGAGAGAGATATATTGCATGATATGGTGAAGATAGTGAAGAAAAAG
upper sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 2
--ctaagatgca--ttctctctgatctgcatataatttacttgtctagatcatttgatgatttgaaaaattcatttggttttctgttggtccattgtattaaagTTGTTGGAGACAATCATAAAGAACTGTGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG
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ccttcagttgtagatttcattcaat---caattgttgcattctcctgcttgcctttatctgatagaggattaaattggttttgcttttgtct-ttctactatagCTATTGGAGACAGTCGTAAAAAACTGTGGAGATATTGTCCATATGCATGTAGCAGAGAGAGATATTCTTCATGAGATGGTGAAAATAGTAAAGAAAAAGMapped 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|17021949|gb|BM092983.1|BM092983EST: AGAAGCGGATTGGAAGTAAAAATTCAAAAGTTCAACTTCTTGCACTAACT TTGTTGGAGACAATCATAAAGAACTGTGGAGATATTGTTCACATGCATGTT
genomic: AGAAGCGGATTGGAAGTAAAAATTCAAAAGTTCAACTTCTTGCACTAACTgtaagcaaga ... tgtattaaagTTGTTGGAGACAATCATAAAGAACTGTGGAGATATTGTTCACATGCATGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttgatgatttgaaaaattcatttggttttctgttggtccattgtattaaagTTGTTGGAGACAATCATAAAGAACTGTGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG
atttgat putative branch site (score: 5)
atttgaaaaattcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaagatgcattctctctgatctgcatataatttacttgtctagatcatttgatgatttgaaaaattcatttggttttctgttggtccattgtattaaagTTGTTGGAGACAATCATAAAGAACTGTGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - -gcattct
- - - - - - - - - - - tgcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg