Sequence
atgc intronic sequence ATGC exonic sequencegtaaagttccatgatagaagagatctttatgttctagttctagacatgttctcagtttctggcactgaagcaatatgcgaagcatcctaccgttccctgttttggagttttttttttttttttttgtatgtcttcccaatcatttgcttgttgggctgatgcatgcgtatcttgcagGGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATGCGCAATATTGATGATAG
Basic information
species | Glycine max |
transcript | GLYMA09G18840.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 3
gtaaagttccatgatagaagagatctttatgttctagttctagacatgttctcagtttctggcactgaagcaatatgcgaagcatcctaccgttccctgttttggagttttttttttttttttttgtatgtcttcccaatcatttgcttgttgggctgatgc-atgcg-tatcttgcagGGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATGCGCAATATTGATGATAG
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-------------------------------------------------------------------------------gtacttactttgatccctcatttgcattgtctttctgtaatagttaataaaagctaatggcttatcctcttctaacttgttgttatgggctggattgcagGGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATGCGCAACATTGATGACAG
upper sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G136815_T01 (Zea mays), 3'ss of exon 3
gtaaagttccatgatagaagagatctttatgttctagttctagacatgttctcagtttctggcactgaagcaatatgcgaagcatcctaccgttccctgttttggagttttttttttttttttttgtatgtcttcccaatcatttgcttgttgggctgatgcatgcgtatcttgcagGGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATGCGCAATATTGATGATAG
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----------------------------gtatgccacttc----cccgttc--gatctccagaatataaataccacgaagaaca----atggatcca------gaacatatatatacttgtgatgacaaatcgcc----tgctgtgctttctgga--aatgaac---tgttgttcagGGGTTTGACAACCTGAGAAGCCAGAGTGTGGCGCCTCCACAATGGACCATGCGCAACAAAGACGACAG
upper sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 3
gtaaagttccatgatagaagagatctttatgttctagttctagacatgttctcagtttctggcactgaagcaatatgcgaagcatcctaccgttccctgttttggagttttttttttttttttttgtatgtcttcccaatcatttgcttgttgggctgatgcatgcgtatcttgcagGGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATGCGCAATATTGATGATAG
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------------------------------------------------------------------------gtatgtactttgatctctttcgcaatgcttctggtggagtatctgaagagaacatcggttatatccattactaactcttta---tgttttatgtccggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAG
upper sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 3
gtaaagttccatgatagaagagatctttatgttctagttctagacatgttctcagtttctggcactgaagcaatatgcgaagcatcctaccgttccctgttttggagttttttttttttttttttgtatgtcttcccaatcatttgcttgttgggctgatgcatgcgtatcttgcagGGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATGCGCAATATTGATGATAG
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---------------------------------------------------------------------gcaaaatgaattcaatttttcctgttgaggctctaaacttagatttgtggtttctc------catcatattcttttaccctttg--ctgttgattgaatgtcatatagGGATTTGATAATCTCAGAAGCCAGAGTGTCGCTCCACCTCAGTGGACAATGCGCAATATTGATGACAGMapped 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|193511596|gb|FK471763.1|FK471763EST: CAAAAGTGGAAGTTGTAGCAAATGATCCCAGTGGATGTACATTTACTCTG GGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATG
genomic: CAAAAGTGGAAGTTGTAGCAAATGATCCCAGTGGATGTACATTTACTCTGgtaaagttcc ... tatcttgcagGGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtatgtcttcccaatcatttgcttgttgggctgatgcatgcgtatcttgcagGGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATGCGCAATATTGATGATAG
ggctgat putative branch site (score: 4)
aatcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagttccatgatagaagagatctttatgttctagttctagacatgttctcagtttctggcactgaagcaatatgcgaagcatcctaccgttccctgttttggagttttttttttttttttttgtatgtcttcccaatcatttgcttgttgggctgatgcatgcgtatcttgcagGGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATGCGCAATATTGATGATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC