Sequence
atgc intronic sequence ATGC exonic sequence...ttcctaatttatattaagagaatggtagatgttaaagcattataattttaaagattacttaatcaaaatctcataattcacttgatgaacttttttgcagACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCTCGTCCACTAAAGGATGTTATTCTTGTTTCTTATGAGATCATTCACAAGA
Basic information
species | Glycine max |
transcript | GLYMA20G02880.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 3
---ttcctaattt--atattaagagaatggtagatgttaaagcattataattttaaagattacttaatcaaaatctcataattcacttgatgaacttttttgcagACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCTCGTCCACTAAAGGATGTTATTCTTGTTTCTTATGAGATCATTCACAAGA
| | | || | || ||| ||| || |||| | |||| | | | | | || | | || |||||| | ||| | || || ||||| ||||| || || || |||||| | ||||| || ||||||||||| ||| | || | || ||||||||||| |||||||||||||| ||||| || |
gattgcatgatcttaattttactcctatgttaagtgtt---gtcctatagatctgtacctgtttgaagagagaacttataatttg--tactgaccgttcttacagACAATTGCCACAGTTTGCATGTTCTTGGCTGGAAAAGTTGAAGAGACGCCTAGGCCTTTGAAAGATGTTATTCTGGTTTCTTATGAGATTATTCATAAAA
upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G45190.1 (Arabidopsis thaliana), 3'ss of exon 3
ttcctaatttatattaagagaatggtagatgttaaagcat----tataattttaaagattacttaatcaaaatctcataattcacttgatgaacttttttgcagACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCTCGTCCACTAAAGGATGTTATTCTTGTTTCTTATGAGATCATTCACAAGA
|| | | | || |||| || |||| | || | ||| | |||| || | || ||| ||| ||| |||||||||||||||| || || |||||||||||||| |||||||| || ||||| || || | || ||||||||| |||| || |||||||| || ||||||
---tctatgcagaattagtgaattgtgattgttgttatttcttctagagcggaaaaaaatactcggatctttactgagctctctcttcatgt-tgtttctgcagACCATTGCAACTGTATGCATGTTCCTTGCTGGAAAGGTTGAGGAAACTCCACGGCCCTTGAAAGATGTTATTTTTGTCTCCTATGAGATTATAAACAAGA
upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 4
----ttcctaatttatattaagagaatggtagatgttaaagcattataattttaaag--attacttaatcaaaatctcataattcacttgatgaacttttttgcagACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCTCGTCCACTAAAGGATGTTATTCTTGTTTCTTATGAGATCATTCACAAGA
||| | | ||||| | | |||| || ||| | | | |||| |||||| | || | ||| | || | | ||||| ||||| || ||||| ||||||||||| || || || ||||| |||||| | || |||| ||||||||| |||| || |||||||| || |||||||
ctagttctttgtccatatttatc--cttctagaaactagcgcagaacagtattaagattattactgagtcctttttccatgttgtcctccct----cctcacccagACGATTGCTACAGTCTGCATGTTCCTTGCGGGAAAAGTGGAAGAAACTCCTAGGCCGTTAAAAGATGTTATTGTTGTCTCCTATGAGATAATACACAAGA
upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G19560.1 (Arabidopsis thaliana), 3'ss of exon 3
ttcctaatttatattaagagaatggtagatgttaaagcattat--aattttaaagattacttaatcaaaatctcataattcacttgatgaactt-ttttgcagACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCTCGTCCACTAAAGGATGTTATTCTTGTTTCTTATGAGATCATTCACAAGA
||| || | | | | | || | || | || ||| | ||| | | | | || | || | | || | | ||||| |||||||| ||||| ||| |||| |||||||||||||| || ||||| || || | || |||||| ||| || ||||||| || |||||||
---gtaaatttttgtgcttgttttgcgatgattgtattcttcttgaaaagtaagaacaactagactagtacttatgcctttgcctgttacatttgctctccagACGATTGCAACAGTCTGCATGCTCCTAGCTGGGAAGGTTGAGGAAACTCCAGTGACATTAGAAGACGTTATTATTGCCTCATATGAGAGAATACACAAGA
upper sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 2
ttcctaatttatattaagagaatggtagatgttaaagcattat-----aattttaaagattacttaatcaa---aatctcataattcacttgatgaactt-ttttgcagACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCTCGTCCACTAAAGGATGTTATTCTTGTTTCTTATGAGATCATTCACAAGA
| || |||| |||||| || | | || | || | || | | | | ||| || | ||| | | | ||| |||||||| || || || || |||||||| || |||||||||||||||||||| || ||||| ||||||||||| |||||||| ||||| || ||||| || |
---------tgcatgggaagaaaagtagataaaaatgaaatacgcaagagattagttggttttgcatttgatccattcttatcgctaccttctttcatatgctttacagACCATCGCCACAGTATGCATGTTCCTCGCAGGGAAGGTTGAAGAGACTCCACGCCCACTGAAGGATGTTATCCTTGTTTCCTATGAAATAATTCATAAAAMapped 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|14258937|gb|BG881845.1|BG881845EST: CGCAAGTCATACTGCACATTCTTGCAGGATTTAGGCATGAGACTTAAAGT ACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCT
genomic: CGCAAGTCATACTGCACATTCTTGCAGGATTTAGGCATGAGACTTAAAGTgtgagtttgg ... ttttttgcagACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaaagattacttaatcaaaatctcataattcacttgatgaacttttttgcagACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCTCGTCCACTAAAGGATGTTATTCTTGTTTCTTATGAGATCATTCACAAGA
cttttttgc CT-rich tract
attacttaatcaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcctaatttatattaagagaatggtagatgttaaagcattataattttaaagattacttaatcaaaatctcataattcacttgatgaacttttttgcagACCATTGCAACGGTCTGTATGTTCCTTGCTGGGAAGGTTGAAGAGACTCCTCGTCCACTAAAGGATGTTATTCTTGTTTCTTATGAGATCATTCACAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaatc