Sequence
atgc intronic sequence ATGC exonic sequence...tcatttaacttctgaatcaatgttttgtaggtaattaattagaatataaaaatcaaataatgtcattgtaataatattaagctcaccttactctttatagGAACTGTGAGATTTAATCTTGATCCATTTAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
Basic information
species | Glycine max |
transcript | GLYMA13G29180.1 |
intron # | 23 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G29180.1 (Glycine max), 3'ss of exon 23
lower sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
tcatttaacttctgaatcaatgttttgtaggtaattaattagaatataaaaatcaaataatgtcattgtaataatattaagctcaccttactctttatagGAACTGTGAGATTTAATCTTGATCCATTTAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
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---gtttgtttgtgaaaatacatgatatatcttctcgtttgcttttcttacatcata-aatgttttttt--tggtacta-------------ttgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA
upper sequence: GLYMA13G29180.1 (Glycine max), 3'ss of exon 23
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 23
tcatttaacttctgaatcaatgttttgtaggtaattaattagaatataaaaatcaaataatgtcattgtaataatattaagctcaccttactctttatagGAACTGTGAGATTTAATCTTGATCCATTTAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
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-------gtatgctagtgaaaaatacat--gttagctgctggagcttctttttttggcaacttgggtttagtgaaat---atttattaatgccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA
upper sequence: GLYMA13G29180.1 (Glycine max), 3'ss of exon 23
lower sequence: AT1G30400.1 (Arabidopsis thaliana), 3'ss of exon 24
-----tcatttaacttctgaatcaatgttttgtaggtaattaattagaatataaaaatcaaataatgtcattgtaata-atattaagctcaccttactctttatagGAACTGTGAGATTTAATCTTGATCCATTTAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
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gtatgtcttgcatttcttctggtgcttatatttattttcctgcttctggtatttatctttcttaaagtcaaaataatgtatactatgccaataacttatatta-agGTACCGTGAGATTCAATCTTGACCCATTTAGTGAACACAACGACGCCGATCTCTGGGAATCTCTTGAGAGGGCACACTTGAAAGATACTATCCGCAGAAA
upper sequence: GLYMA13G29180.1 (Glycine max), 3'ss of exon 23
lower sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 23
----tcatttaacttctgaatcaatgttttgtaggtaattaattagaatataaaaatcaaataatgtcattgtaataatattaagctcaccttactctttatagGAACTGTGAGATTTAATCTTGATCCATTTAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
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attactgataagatcctaagttatcaattcaatacattttagttaataaattttttttaa-tgaagt--ttgtgttattctaatgatcac-ttgtttcacatagGAACTGTGCGATTCAATCTTGATCCTTTCAACGAGCACAATGATGCTGACCTCTGGGAGGCTTTAGAGAGGGCACATTTGAAGGATGTTATCAGGAGGAAMapped 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|193420889|gb|FK387060.1|FK387060EST: TTTGCGTAAAGTTCTTGGCATTATACCACAATCTCCTGTTCTCTTTTCAG GAACTGTGAGATTTAATCTTGATCCATTTAATGAACACAATGATGCTGACC
genomic: TTTGCGTAAAGTTCTTGGCATTATACCACAATCTCCTGTTCTCTTTTCAGgtatttatga ... ctctttatagGAACTGTGAGATTTAATCTTGATCCATTTAATGAACACAATGATGCTGACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaaaatcaaataatgtcattgtaataatattaagctcaccttactctttatagGAACTGTGAGATTTAATCTTGATCCATTTAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
accttac putative branch site (score: 3)
ctcaccttactcttt CT-rich tract
aatcaaataatgtcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatttaacttctgaatcaatgttttgtaggtaattaattagaatataaaaatcaaataatgtcattgtaataatattaagctcaccttactctttatagGAACTGTGAGATTTAATCTTGATCCATTTAATGAACACAATGATGCTGACCTCTGGGAGGCTCTGGAGAGGGCACATTTGAAGGATGTGATACGGAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - -acttctg
- - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - -ataaaaa