Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcatcaaagagagggagagaatctgtggaaaggcattatcttatctcgaacagtcgcgtgataccttatcttctacagttcttaattagtgagtattttatcaatcttgaactggtataatttagctaattaatgtttatgttaatatagATGACCAATTTAACCAAGGAAGAGTTTGTCCACGTACTTCGCCGACAAAGCACTGGATTTCCCAGAGGAAGCTCCAAATATAGAGGTGTAACTTTGCACA
Basic information
species | Glycine max |
transcript | GLYMA11G05720.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G05720.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G36920.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtcatcaaagagagggagagaatctgtggaaaggcattatcttatctcgaacagtcgcgtgataccttatcttctacagttcttaattagtgagtattttatcaatcttgaactggtataatttagctaattaatgtttatgttaa----tatagATGACCAATTTAACCAAGGAAGAGTTTGTCCACGTACTTCGCCGACAAAGCACTGGATTTCCCAGAGGAAGCTCCAAATATAGAGGTGTAACTTTGCACA
| | || | || || | |||||| || || | | ||| | |||||| || | || | |||||||||| |||||||||||||||||||| || ||||||||||||||||||||||| || || || ||||||| || || ||||||||||| |||||||| |
------------------------------------------------------------------------gtaaatataaattataaactatattggtttttattaac---gatttttaaaggtttgggagattaatattgaaattgaattttatagATGACTAATTTAACCAAGGAAGAGTTCGTACACGTACTTCGCCGACAAAGCACAGGCTTCCCTCGAGGAAGTTCGAAGTATAGAGGTGTCACTTTGCATA
upper sequence: GLYMA11G05720.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G67180.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtcatcaaagagagggagagaatctgtggaaaggcattatcttatctcgaacagtcgcgtgataccttatcttctacagttcttaattagtgagtattttatcaatcttgaactggtataatttagctaattaatgtttatgttaatatagATGACCAATTTAACCAAGGAAGAGTTTGTCCACGTACTTCGCCGACAAAGCACTGGATTTCCCAGAGGAAGCTCCAAATATAGAGGTGTAACTTTGCACA
| ||| | | | | |||| | ||| | || | | | | | ||| | || | | ||| | ||| | ||| | || | ||||| ||||| || |||||||||||| | || |||||| | | ||||||||||| ||||| ||||| || || ||||| |||||||| ||||||||||
------------------------------------------gttctatataagtcttttatg-gatatatctactttaggttatactagtaatttaattacttactactcagaagaaaacacaatgaaat--attggttttttt-tttttgcagATGGGAAATTTGACAAAGGAAGAGTTTATGCATGTACTTAGAAGGCAAAGCACTGGGTTTCCAAGAGGCAGTTCTAAATACAGAGGTGTTACTTTGCACA
upper sequence: GLYMA11G05720.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0031g00220.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtcatcaaagagagggagagaatctgtggaaaggcattatcttatctcgaacagtcgcgtgatac------cttatcttctacagttcttaattagtgagtattttatcaatcttgaactggtataatttagctaattaatgttta-tgttaa---tatagATGACCAATTTAACCAAGGAAGAGTTTGTCCACGTACTTCGCCGACAAAGCACTGGATTTCCCAGAGGAAGCTCCAAATATAGAGGTGTAACTTTGCACA
| | | | | | | | | | | | ||||||| ||||| |||| | || || | |||| || ||| | || || ||| | || ||| | | | | || |||| | | ||||| |||| ||||||||||||||||||| || || |||||||||||||| ||||| ||||| |||||||||||||| |||||||||||||| || ||||
-------gtagagaggggcttcaccttatcttgtacagttccaccttatcttctacagtattttgattcgcttttctgattgttgctagttgagaaatagcaaaaatgaagaaaaaaaagaaagtggattgtttttcatgtatacatgtaatgttgaatgcacagATGGGCAATCTAACCAAGGAAGAGTTTGTGCATGTCCTTCGCCGACAAAGTACTGGTTTTCCGAGAGGAAGCTCCAAGTATAGAGGTGTAACCTTACACAMapped 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|15815383|gb|BI787658.1|BI787658EST: AGGCAGACATCAACTTCAACATCGAAGACTATGAGGAAGACTTGAAGCAG ATGACCAATTTAACCAAGGAAGAGTTTGTCCACGTACTTCGCCGACAAAGC
genomic: AGGCAGACATCAACTTCAACATCGAAGACTATGAGGAAGACTTGAAGCAGgtgagtcatc ... gttaatatagATGACCAATTTAACCAAGGAAGAGTTTGTCCACGTACTTCGCCGACAAAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatcaatcttgaactggtataatttagctaattaatgtttatgttaatatagATGACCAATTTAACCAAGGAAGAGTTTGTCCACGTACTTCGCCGACAAAGCACTGGATTTCCCAGAGGAAGCTCCAAATATAGAGGTGTAACTTTGCACA
tgttaat putative branch site (score: 3)
tataatttagctaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcatcaaagagagggagagaatctgtggaaaggcattatcttatctcgaacagtcgcgtgataccttatcttctacagttcttaattagtgagtattttatcaatcttgaactggtataatttagctaattaatgtttatgttaatatagATGACCAATTTAACCAAGGAAGAGTTTGTCCACGTACTTCGCCGACAAAGCACTGGATTTCCCAGAGGAAGCTCCAAATATAGAGGTGTAACTTTGCACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA