Sequence
atgc intronic sequence ATGC exonic sequence...gaaactgtcatcataatttgttgtaagcatagaattactgatttttgtaatcaatgatcacaagattttgacatctattaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
Basic information
species | Glycine max |
transcript | GLYMA15G11890.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 3
----gaaactgtcatcataatttgttgtaagcatagaattactgatttttgtaatcaatgatcacaagattttgacatctattaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
|| | || || || || | || || || | || | || || | | || | ||| | | | || ||||||| ||||| ||||| |||||||| ||||||||||||||||| |||||||||
tgctgatggttaggtcgctgcatgaaatatacacacttttcctttttaaggggctctcttatttcagg--tacgattttaatt--ttgtttctctttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 3
gaaactgtcatcataatttgttgtaagcatagaat-tactgatttttgtaatcaatgatcacaagattttgac-atctattaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
||||| | | | | || || | | | |||| || || | |||||| || ||||| || | ||| || ||||||| ||||| ||||| |||||||| ||||||||||||||||| || ||||||
-aaacttctttaacacacacacacacatatgacatatgtatgtatgtgtacacacacattatttccttttgatgatgcattaa-aattttgtctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 3
gaaactgtcatcataatttgttgtaagcatagaattactgatttttg--taatcaatgatcacaagattttgacatctattaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
||| | ||||||| | |||| || | | || | | || || || | | || | | || | | ||| | ||||||||| ||||| ||||| || ||||| || ||||||||||||||||||||||||
caaattttcatcatgaagagttggaactaaaagctttgttacttaaagatatgcattttgtgtttattcttagtagtttttgttgtgagtctct--ttgcagGGTGGATTTGATATGATATGTAGTGGAAGAGACAAGATTGAAACTCCAGAGCAG
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------gaaactgtcatcataatttgttgtaagcatagaattactgatttttgtaat-caatgatcacaagattttgacatctattaataaccatttctgct---ggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
| || | | | | | | | || |||| | || | ||| | | || | | || | | | | ||| || | |||||||| ||||||||||| |||||||| || |||||||||||||| || || |||
gtacttggattcagatccttccacaagatttgaatttacactccactagatgtggagcattagtccttggttaaatatacttgtctttttaagtcgatgtggttataattctttttttggtctcaacagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG
upper sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 3
gaaactgtcat-cataatttgt---tgtaagcatagaattactgatttttgtaatcaatgatcacaagattttgacatctattaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
| ||| || | ||| | ||| ||| | || | ||| || | | | | || | |||| | | | | | | |||||||| ||||| ||||| ||||||||||| |||||||||||||||||||| |||
---gcattcacgcacattttatctatgtgctcatgtatgcacacaggcatgtgat-accaccaatatagcctcaacttgtattctttgtcttgttttatatcagGGTGGTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAGMapped 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|16347925|gb|BI973520.1|BI973520EST: GCAAATACGTTGAACTCACTTCTGAATATATTTATCCTTATAGAAATCAG GGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAG
genomic: GCAAATACGTTGAACTCACTTCTGAATATATTTATCCTTATAGAAATCAGgtccgttttc ... ctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAG
EST:
gi|17021880|gb|BM092914.1|BM092914EST: GCAAATACGTTGAACTCACTTCTGAATATATTTATCCTTATAGAAATCAG GGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAG
genomic: GCAAATACGTTGAACTCACTTCTGAATATATTTATCCTTATAGAAATCAGgtccgttttc ... ctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaatcaatgatcacaagattttgacatctattaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
taataac putative branch site (score: 1)
ccatttct CT-rich tract
tattaataaccattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaactgtcatcataatttgttgtaagcatagaattactgatttttgtaatcaatgatcacaagattttgacatctattaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- -actgtca
- - - - - - - - - - -tgtaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacatc