Sequence
atgc intronic sequence ATGC exonic sequence...acgtttatttagtgttgaaggccagagtaaattctgtgagagagaaaaaaatacttgtcatttaaatgggtgaatgattattacctattttgttttgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCCAAG
Basic information
species | Glycine max |
transcript | GLYMA17G16630.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G16630.3 (Glycine max), 3'ss of exon 3
lower sequence: AT5G46630.2 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------acgtttatttagtgttgaaggccagagtaaattctgtgagagagaaaaaaatacttgtcatttaaatgggtgaatgattattacctattttgttttgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCCAAG
| | ||| | | | | | ||| | | | | || || | | | |||||||| || | | ||| ||||||| |||||||||||||| || ||||||||||| ||||| || || ||||| |||||||||||||||||||| || || || ||||||||||| |||
gtaagtaagcctgatagggtcatgatcaaatcactttcttatcacttgtaaagttgcattagtcgttatatgttattctattttgtggtaacaccaatgaatgatattt---tgtattgaattgcagAGATTATGGACTTTGGCTATCCACAAAATCTCTCACCTGAAATTTTAAAACTTTATATCACTCAGGAAGGTGTACGGTCACCATTTTCATCGAAG
upper sequence: GLYMA17G16630.3 (Glycine max), 3'ss of exon 3
lower sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 3
----acgtttatttagtgttgaaggccagag--taaattctgtgagagagaaaaaaatacttgtcatttaaatgggtgaatgattattacctattttgttt-tgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCCAAG
| | || | || | | | || | | ||||||| | | | | || | || | || ||| | || || |||||| |||||||| ||||| || || ||||| | || |||||||| || || |||||||| ||||| ||||| || ||||| |||||||||||||||
atccagtgtcatctcgtcataatgaccgcacgtttaattctgaagtcgcctccccagtcttcgttacc-------atgtgcaactaacaccactgttattcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG
upper sequence: GLYMA17G16630.3 (Glycine max), 3'ss of exon 3
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 3
acgtttatttagtgttgaaggccagagtaaattctgtgagagagaaaaaaatacttgtcatttaaatgggtgaatgatt-attacctattttgttttgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCCAAG
|| || || ||| | || | ||| || || ||| | |||||| || ||||||||||| ||||| ||||||||||| || ||||| || ||||| ||||| |||||||| || || ||||| ||||| || |||
--------------------------------------------------gtattt-tcgtttggtttcatggaaaattcatcacgcttttgaatgtgcagAGATCATGGACTTTGGATACCCGCAAAATCTTTCTCCTGAGATTTTGAAGCTCTATATAACTCAGGAGGGTGTTCGTTCGCCATTCTCG---AAG
upper sequence: GLYMA17G16630.3 (Glycine max), 3'ss of exon 3
lower sequence: EFJ25669 (Selaginella moellendorffii), 3'ss of exon 3
acgtttatttagtgttgaaggccagagtaaattctgtgagagagaaaaaaatacttgtcatttaaatgggtgaatgatt-attac-ctattttgttttgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCCAAG
|| || || ||| | | | ||| || || || || | |||||| || ||||||||||| ||||| ||||||||||| || ||||| || ||||| ||||| |||||||| || || ||||| ||||| || |||
--------------------------------------------------gtattt-tcgtttggtttctcggaaaattcatcacacttttgaaatgtgcagAGATCATGGACTTTGGATACCCGCAAAATCTTTCTCCTGAGATTTTGAAGCTCTATATAACTCAGGAGGGTGTTCGTTCGCCATTCTCG---AAGMapped 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|209699279|gb|BW670241.1|BW670241EST: CGAGGATGCAATTCGCAATAATTTTGTACTCATTTATGAGCTCCTAGATG AAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGC
genomic: CGAGGATGCAATTCGCAATAATTTTGTACTCATTTATGAGCTCCTAGATGgtatgcaatt ... tgttttgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaaatacttgtcatttaaatgggtgaatgattattacctattttgttttgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCCAAG
ttttgtttt CT-rich tract
attattacctatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acgtttatttagtgttgaaggccagagtaaattctgtgagagagaaaaaaatacttgtcatttaaatgggtgaatgattattacctattttgttttgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG