Sequence
atgc intronic sequence ATGC exonic sequence...tctccataatttgttgtaagagaaacattactgattttgttaaattataatcaatgatcattagattttgacatcttttaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
Basic information
species | Glycine max |
transcript | GLYMA09G01050.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 3
tctccataatttgttg--taagagaaacattactgattttgttaaattataatcaatgatcattagattttgacatcttttaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
| || || | | | |||| || |||| | | | | | | || | || | || | | | || ||||||| ||||| ||||| |||||||| ||||||||||||||||| |||||||||
tgctgatggttaggtcgctgcatgaaatatacacacttttcctttttaaggggctctcttatttcaggtacgattttaatt--ttgtttctctttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 3
---tctccataatttgttgtaagagaaacattactgattttgttaaattataatcaatgatcattagattttgacatcttttaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
|| ||| | | | | || || || | || | || || || ||| |||||| | | || | ||| || ||||||| ||||| ||||| |||||||| ||||||||||||||||| || ||||||
aaacttctttaacacacac--acacacatatgacatatgtatgtatgt-gtacacacacattatttccttttgatgatgcattaaaattttgtctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 3
-------tctccataatttgttgtaagagaaacattactgattttgttaaattataatcaatgatcattagattttgacatcttttaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
|| ||| | |||| || ||| || | || | || ||| || | || | || | |||| | | ||| | ||||||||| ||||| ||||| || ||||| || ||||||||||||||||||||||||
caaattttcatcatgaagagttggaactaaaagctt-----tgttacttaaagatatgcattttgtgtttattcttagtagtttttgttgtgagtctct--ttgcagGGTGGATTTGATATGATATGTAGTGGAAGAGACAAGATTGAAACTCCAGAGCAG
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------tctccataatttgttgtaagagaaacattactgattttgttaaattataatcaatgatcattagattttgacatcttttaataaccatttctgct---ggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
| | | | | | | | | ||||| | ||| | || |||| | || || | | || | || | | ||| || | |||||||| ||||||||||| |||||||| || |||||||||||||| || || |||
gtacttggattcagatccttccacaagatttgaatttacactccactagatgtggagcatta--gtccttggttaaatatacttg----tctttttaagtcgatgtggttataattctttttttggtctcaacagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG
upper sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 3
---tctccata-atttgttgtaagagaaacattactgattttgttaaattataatcaatgatcattagattttgacatcttttaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
| | | |||| | || | | || | | | | ||| | | | || | || | | || | | | | | | |||||||| ||||| ||||| ||||||||||| |||||||||||||||||||| |||
gcattcacgcacattttatctatgtgctcatgtatgcacacaggcatgtgata--ccaccaatat--agcctcaacttgtattctttgtcttgttttatatcagGGTGGTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAGMapped 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|5342441|gb|AI794725.1|AI794725EST: GCANATACGTTGAGCTCACCTCTGAATATATTTATCCTTATAGAAATCAG GGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAG
genomic: GCAAATACGTTGAGCTCACCTCTGAATATATTTATCCTTATAGAAATCAGgtttgttttc ... ctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAG
EST:
gi|15204845|gb|BI427613.1|BI427613EST: GCAAATACGTTGAGCTCACCTCTGAATATATTTATCCTTATAGAAATCAG GGTGGCTTTGACATGATTTGCAGTGGGAGGGACNAGATTGAAACTCCAGAG
genomic: GCAAATACGTTGAGCTCACCTCTGAATATATTTATCCTTATAGAAATCAGgtttgttttc ... ctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataatcaatgatcattagattttgacatcttttaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
taataac putative branch site (score: 1)
ccatttct CT-rich tract
ttttaataaccattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctccataatttgttgtaagagaaacattactgattttgttaaattataatcaatgatcattagattttgacatcttttaataaccatttctgctggcagGGTGGCTTTGACATGATTTGCAGTGGGAGGGACAAGATTGAAACTCCAGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - -tgttgta
- - - - - - - - - -gagaaac