Sequence
atgc intronic sequence ATGC exonic sequencegttttctttccatcttactcatccattatgttctcatcatttcatgttttaaggtcttttctggctttccttttcccacatgcgtctaggatttgatggtaggctgatcatttttcagACTATTAACAATGATGATTTGGAGGAGATCCGTGAGCTTGGTTCTGGAACCTATGGAGCTGTTTATCATGGGAAATGGAAAGGTTCTGACGTTGCCATTA
Basic information
species | Glycine max |
transcript | GLYMA13G01190.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G01190.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G052658_T01 (Zea mays), 3'ss of exon 2
gttttctttccatcttactcatccattatgttctcatcatttcatgttttaaggtcttttctggctttccttttcccacatgcgtctaggatttgatggtaggctgatcatttttcagACTATTAACAATGATGATTTGGAGGAGATCCGTGAGCTTGGTTCTGGAACCTATGGAGCTGTTTATCATGGGAAATGGAAAGGTTCTGACGTTGCCATTA
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-----------------------------------------gtatgttatgtgatctct----gtgtgaattttactttatgtttc---atttatactgtttatggatcatg---cagACTATAAAAAATGACGATTTGGAGGAAATTAGAGAGCTGGGTTCAGGTACTTATGGGGCAGTTTATCATGGTAAATGGAGAGGATGTGATGTCGCTGTTA
upper sequence: GLYMA13G01190.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 3
gttttctttccatcttactcatccattatgttctcatcatttcatgttttaaggtcttttctggctttccttttcccacatgcgtctaggatttgatggtaggctgatcatttttcagACTATTAACAATGATGATTTGGAGGAGATCCGTGAGCTTGGTTCTGGAACCTATGGAGCTGTTTATCATGGGAAATGGAAAGGTTCTGACGTTGCCATTA
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-----------gtttttattcttaaacccgtcttatagaattctgaaaccgaacaaatttctag---tccttttgactttgttatcttggttttcac------ct--tctttatctagTCTATAAGAAACGATGATTTGGAGGAAATCCGAGAGTTAGGCCATGGAACATATGGATCTGTTTACCATGGAAAATGGAAAGGCTCAGATGTTGCAATAA
upper sequence: GLYMA13G01190.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------gttttctt------tccatctt-actcatccattatgttctcatcatttca-tgttttaaggtcttttctggctttccttttcccacatgcgtctaggatttgatggtaggctgatcatttttcagACTATTAACAATGATGATTTGGAGGAGATCCGTGAGCTTGGTTCTGGAACCTATGGAGCTGTTTATCATGGGAAATGGAAAGGTTCTGACGTTGCCATTA
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gttctcgaccaatatacaccattatttttgtaaaacatctctttggaaatcacacctttatctcttcattatctcttctccatcttagtgtctttttactatttcatgcattttatttcctctgcctaactcgaatttg---------tgttctttctttagACAATAAAAAATGATGATCTGGAGGAGATTCGGGAATTAGGTTCTGGTACGTATGGAGCTGTTTACCATGGAAAATGGAAGGGGTCTGATGTAGCAATAAMapped 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|19269993|gb|BM886249.1|BM886249EST: AAATTGAGTCTACAAGGGCTGAGGAAGAAGCATTTGCTAATGGATTGCAG ACTATTAACAATGATGATTTGGAGGAGATCCGTGAGCTTGGTTCTGGAACC
genomic: AAATTGAGTCTACAAGGGCTGAGGAAGAAGCATTTGCTAATGGATTGCAGgttttctttc ... catttttcagACTATTAACAATGATGATTTGGAGGAGATCCGTGAGCTTGGTTCTGGAACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctttccttttcccacatgcgtctaggatttgatggtaggctgatcatttttcagACTATTAACAATGATGATTTGGAGGAGATCCGTGAGCTTGGTTCTGGAACCTATGGAGCTGTTTATCATGGGAAATGGAAAGGTTCTGACGTTGCCATTA
ggctgat putative branch site (score: 4)
tcatttttc CT-rich tract
atcattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttctttccatcttactcatccattatgttctcatcatttcatgttttaaggtcttttctggctttccttttcccacatgcgtctaggatttgatggtaggctgatcatttttcagACTATTAACAATGATGATTTGGAGGAGATCCGTGAGCTTGGTTCTGGAACCTATGGAGCTGTTTATCATGGGAAATGGAAAGGTTCTGACGTTGCCATTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT