Sequence
atgc intronic sequence ATGC exonic sequence...cttgtttcttctatatatatatatatatacttacttttgaatttcatattttcaccatgtaagtaaaatatttaacttttggaagcaatattgctgacagAATTCTATTGGTGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGCGCATACCTAATG
Basic information
species | Glycine max |
transcript | GLYMA20G32030.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 13
-cttgtttcttctatatatatatatatatacttacttttgaatttcatat-tttcaccatg-taagtaaaatatttaacttttggaagcaatattgctgacagAATTCTATTGGTGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGCGCATACCTAATG
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gttagtttgtactgattgtata-attcaga-ttgtcttgaaatttgttctatttcacctggctgaataaaatgtaagtcattcctggtcaatctttc----agAATACTATTGGTGAGGAGTCACATTTAGCTATGGAAACAAGTGGCCATGGAGCACTGAAAGAGAATCACTGGCTCGATGATGGTGCATATCTTATG
upper sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G069676_T02 (Zea mays), 3'ss of exon 12
-------cttgtttcttctatatatatatatatatacttacttttgaatttcatattttcaccatgtaagtaaaatatttaacttttggaagcaatattgctgacagAATTCTATTGGTGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGCGCATACCTAATG
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tatgtaattgagttagtccctgaatttccatattttaaaatttccgtccctaaaatttttcaagcagtaggatgagatttagaatatggaa--aatttt-----cagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGAGCGCTGAAAGAGAACCACTGGCTTGATGATGGAGCATACCTTATG
upper sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 13
cttgtttcttctatatatatat-atatatacttacttttgaatttcatattttcaccatgta--agtaa-aatatttaacttt--tggaagcaatattgc--tgacagAATTCTATTGGTGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGCGCATACCTAATG
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-------gttagatagagaaaccatacattctggcaggaaaagcttac-tccgccttatggaccattgataattcttatctgaaatagaagttgtgatgtgatggcagAACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAACCAGTGGTCATGGAGCTCTAAAGGAAAACCATTGGCTCGACGATGGGGCCTATCTCATG
upper sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 13
------cttgtttcttctatatatatatatatatacttacttttgaatttcatattttcaccatgtaagtaaaatatttaacttttggaagcaatattgctgacagAATTCTATTGGTGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGCGCATACCTAATG
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tataaacaatcttcttccttgt-cacactttggttacta-ttctgcattttgggtttccactgc-tgag---aatattttaactgaagcagtaatgttgctgacagAATTCTGTTGGTGAGGAGTCACATCTGGCTATTGAGACTAGTGGCCATGGAGCTCTCAAGGAGAATCACTGGCTTGATGATGGTGCATACCTCATGMapped 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|298163368|gb|HO012101.1|HO012101EST: GGTTCAAAAGAGGCTACAAAAATGTGATTGATGAAGCTATTCGTTTG AATTCTATTGGTGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGA
genomic: GGTTCAAAAGAGGCTACAAAAATGTGATTGATGAAGCTATTCGTTTGgtatgatgag ... ttgctgacagAATTCTATTGGTGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattttcaccatgtaagtaaaatatttaacttttggaagcaatattgctgacagAATTCTATTGGTGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGCGCATACCTAATG
atttaac putative branch site (score: 3)
atgtaagtaaaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgtttcttctatatatatatatatatacttacttttgaatttcatattttcaccatgtaagtaaaatatttaacttttggaagcaatattgctgacagAATTCTATTGGTGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGCGCATACCTAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagtaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttttgg