Sequence
atgc intronic sequence ATGC exonic sequence...attcattcttactcacctttgttactcaatcatcaattcatcatattataaacttgtatggattatatagcaaacactaacatttttttttttgttacagAAATTGGATTTCAAGTTTCCCCTATCAGTTTCCTGTGTCCACTTTATCTGTTCATCCATTGGAGCTTATGTGGTAATTAAGTTGCTGAAGCTTAAACCAC
Basic information
species | Glycine max |
transcript | GLYMA06G11850.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G11850.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G127591_T03 (Zea mays), 3'ss of exon 2
attcattcttactcaccttt-gttactcaatcatcaat-tcatcatattataaacttgtatggattatatagcaaacactaacatttttttttttgttacagAAATTGGATTTCAAGTTTCCCCTATCAGTTTCCTGTGTCCACTTTATCTGTTCATCCATTGGAGCTTATGTGGTAATTAAGTTGCTGAAGCTTAAACCAC
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gaggttacctactcatctcccatcatcttatgggtggtgtcaagactcaagagccgtgcccttttgatataataagta--agttgctctctcttctctgcagAAACTGGATTTCAAGTTCCCTCTCACCGTGTCCTGCGTCCACTTCATCTGCTCTTCCATTGGAGCTTACATTGCAATCCATGTCCTCAAGGCGAAACCCC
upper sequence: GLYMA06G11850.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G21870.1 (Arabidopsis thaliana), 3'ss of exon 1
--attcattcttactcacctttgttactcaatcatcaattcatcatattataaacttgtatggattatatagcaaacactaacatttttttttttgttacagAAATTGGATTTCAAGTTTCCCCTATCAGTTTCCTGTGTCCACTTTATCTGTTCATCCATTGGAGCTTATGTGGTAATTAAGTTGCTGAAGCTTAAACCAC
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gtttaaaaagtctcttacttttatcattaaagacttagcctttcgt-ttgt---tttatctgatctgcgtttgaaat-ttggtacctttccttgt-ttgcagAAACTGGATTTCAAGTTTCCATTATCAGTTTCATGTGTTCATTTCATATGTTCGTCGATTGGAGCATACATTGTGATTAAAGTCTTAAAGCTTAAACCTT
upper sequence: GLYMA06G11850.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G77610.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------------attcattcttactcacctttgttactcaa---tcatcaattcatcatat--tataaacttgtatggattatatagcaaacactaacatttttttttt--tgttacagAAATTGGATTTCAAGTTTCCCCTATCAGTTTCCTGTGTCCACTTTATCTGTTCATCCATTGGAGCTTATGTGGTAATTAAGTTGCTGAAGCTTAAACCAC
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gtttcttcttaaccctagaatttttaggttttacttaattgtatttaatacccttttgatctgatctattgatctgatgttgctgatttggaatttggtttcagctt-tatagattggtgataaagttttgatttttttttgttgttgttgcagAAACTGGATTTTAAGTTTCCACTATCGGTTTCATGTGTTCACTTCATATGTTCGTCGATTGGAGCTTACATCGTTATCAAAGTTCTCAAGCTTAAACCATMapped 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|193406355|gb|FK373004.1|FK373004EST: GGTGGGCGTTCAATGTCACCGTCATCATCGTCAACAAGTGGATCTTCCAG AAATTGGATTTCAAGTTTCCCCTATCAGTTTCCTGTGTCCACTTTATCTGT
genomic: GGTGGGCGTTCAATGTCACCGTCATCATCGTCAACAAGTGGATCTTCCAGgttcctgttt ... tttgttacagAAATTGGATTTCAAGTTTCCCCTATCAGTTTCCTGTGTCCACTTTATCTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttataaacttgtatggattatatagcaaacactaacatttttttttttgttacagAAATTGGATTTCAAGTTTCCCCTATCAGTTTCCTGTGTCCACTTTATCTGTTCATCCATTGGAGCTTATGTGGTAATTAAGTTGCTGAAGCTTAAACCAC
cactaac putative branch site (score: 1)
catttttttttttgtt CT-rich tract
aaacactaacattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attcattcttactcacctttgttactcaatcatcaattcatcatattataaacttgtatggattatatagcaaacactaacatttttttttttgttacagAAATTGGATTTCAAGTTTCCCCTATCAGTTTCCTGTGTCCACTTTATCTGTTCATCCATTGGAGCTTATGTGGTAATTAAGTTGCTGAAGCTTAAACCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
-ttcattc
- - - - - -ctcacct
- - - - - - - - - - - - - - - - -caattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaacac