Sequence
atgc intronic sequence ATGC exonic sequencegtaagacatccactggccctcactcaccaccaacatattaagaagtttaactttgtattgttaagttcataagactgtagggctatacaaatgcatttctgaatataatcaatttaacagGTAATGGGACCAAGTGGAAGTGGCAAGACTTCTTTGTTAAGAGCTATGGCTGGTCTATGGAAAACTGGAACTGGAAAGATCACATACTATGTAAAAGGTG
Basic information
species | Glycine max |
transcript | GLYMA08G17110.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G17110.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G54350.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagacatccactggccctcactcaccaccaacatattaagaagtttaactttgtattgttaagttcataagactgtagggctatacaaatgcatttctgaatataatcaatttaacagGTAATGGGACCAAGTGGAAGTGGCAAGACTTCTTTGTTAAGAGCTATGGCTGGTCTATGGAAAACTGGAACTGGAAAGATCACATACTATGTAAAAGGTG
| || |||||| | || ||| | | | | | || | | | || || | ||||||||| ||||||| || ||||| ||||| || ||||| || ||||||| ||||||||||| |||| | || | ||||| ||||| | ||| | | ||
-----------------------------------------gttagttcactttgactacttgtgtttaaagcatgtgactggtagattggaagttacttaaaaatg--ccatttaacagATAATGGGTCCTAGTGGGAGTGGAAAAACTTCGCTGCTAAGAGCAATGGCTGGTCTTTGGAGGTCAGGGAAAGGAAAAATCACGTTCTACCTCGATCCTG
upper sequence: GLYMA08G17110.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0085g01190.t01 (Vitis vinifera), 3'ss of exon 7
gtaagacatccactggccctcactcaccaccaacatattaagaagtttaactttgtattgttaagttcataagactgtagggctatacaaatgcatttctgaatataatcaatttaacagGTAATGGGACCAAGTGGAAGTGGCAAGACTTCTTTGTTAAGAGCTATGGCTGGTCTATGGAAAACTGGAACTGGAAAGATCACATACTATGTAAAAGGTG
| ||||| ||| | || ||| ||| ||| | || | || |||| ||||||||||| ||||| ||||| ||||| ||||||||||||||| ||||| |||||||||| |||| ||||||| ||||| ||||||| | ||| |||||||
--------------------------------gttagtggttctgtttacattttccatcctaggttggtaaacttgtcaa-tgaagcagttattcacttgtgtatagctgcattaacagGTAACAGGACCTAGTGGGAGTGGTAAGACTTCTTTGTTACGAGCTCTGGCTGGTCTTTGGAGTACTGGAAGAGGAAAAATCACATTTTCTGTGAAAGGTG
upper sequence: GLYMA08G17110.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ13543 (Selaginella moellendorffii), 3'ss of exon 6
gtaagacatccactggccctcactcaccaccaacatattaagaagtttaactttgtattgttaagttcataagactgtagggctatacaaatgcatttctgaatataatcaatttaa---cagGTAATGGGACCAAGTGGAAGTGGCAAGACTTCTTTGTTAAGAGCTATGGCTGGTCTATGGAAAACTGGAACTGGAAAGATCACATACTATGTAAAAGGTG
|| ||| || ||| || | || | | |||||| ||||| ||||||| || || ||||||||||||||||| || || ||||||||||| || || ||||||||| | || |||| || || | | |
------------------------------------------------------gt-ctgtgaatttctcaaagttt-----cttcgttgctat-ctgatgaataactcgggtttaagaccagGTAACTGGCCCCAGTGGAAGTGGCAAGACATCGTTCTTAAGAGCTATCGCAGGACTATGGAAATCCGGGCAAGGAACCATAGCAAGAAACTCTACCATGG
upper sequence: GLYMA08G17110.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ11675 (Selaginella moellendorffii), 3'ss of exon 7
gtaagacatccactggccctcactcaccaccaacatattaagaagtttaactttgtattgttaagttcataaga---ctgtagggctatacaaatgcatttct-gaatataatcaatttaacagGTAATGGGACCAAGTGGAAGTGGCAAGACTTCTTTGTTAAGAGCTATGGCTGGTCTATGGAAAACTGGAACTGGAAAGATCACATACTATGTAAAAGGTG
|| ||| || ||| || || ||||| || ||| || || | | ||| | ||||||| || || ||||||||||||||||| || || ||||||||||| || || ||||||||| | || |||| || || | | |
------------------------------------------------------gt-ctgtgaatttctcaaagtttcttcgttgctat-cagatgaataactcgggtttaag------accagGTAACTGGCCCCAGTGGAAGTGGCAAGACATCGTTCTTAAGAGCTATCGCAGGACTATGGAAATCCGGGCAAGGAACCATAGCAAGAAACTCTACCATGG
upper sequence: GLYMA08G17110.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ13542 (Selaginella moellendorffii), 3'ss of exon 7
gtaagacatccactggccctcactcaccaccaacatattaagaagtttaactttgtattgttaagttcataaga---ctgtagggctatacaaatgcatttct-gaatataatcaatttaacagGTAATGGGACCAAGTGGAAGTGGCAAGACTTCTTTGTTAAGAGCTATGGCTGGTCTATGGAAAACTGGAACTGGAAAGATCACATACTATGTAAAAGGTG
|| ||| || ||| || || | ||||| || ||| || || | | ||| | ||| ||| || || ||||||||||||||||| || || ||||||||||| || || ||||||||| | || |||| || || | | |
------------------------------------------------------gt-ctgtgaatttctcaaagtttctttgttgctat-cagatgaataactcgggtttaag------accagATAACTGGCCCCAGTGGAAGTGGCAAGACATCGTTCTTAAGAGCTATCGCAGGACTATGGAAATCCGGGCAAGGAACCATAGCAAGAAACGCTGCCATGGMapped 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|120493638|gb|EH221805.1|EH221805EST: ACTTATTAGAGACTTGTCATTGACGATCAAGGAAAAGGATAAGTTTACTG GTAATGGGACCAAGTGGAAAGTGGCAAGACTTC
genomic: ACTTATTAGAGACTTGTCATTGACGATCAAGGAAAAGGATA-GTTTACTGgtaagacatc ... aatttaacagGTAATGGGACCAAGTGGAA-GTGGCAAGACTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcataagactgtagggctatacaaatgcatttctgaatataatcaatttaacagGTAATGGGACCAAGTGGAAGTGGCAAGACTTCTTTGTTAAGAGCTATGGCTGGTCTATGGAAAACTGGAACTGGAAAGATCACATACTATGTAAAAGGTG
atttctgaatataatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagacatccactggccctcactcaccaccaacatattaagaagtttaactttgtattgttaagttcataagactgtagggctatacaaatgcatttctgaatataatcaatttaacagGTAATGGGACCAAGTGGAAGTGGCAAGACTTCTTTGTTAAGAGCTATGGCTGGTCTATGGAAAACTGGAACTGGAAAGATCACATACTATGTAAAAGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA