Sequence
atgc intronic sequence ATGC exonic sequencegttcctacttttctgaatcttatgagattgctgtatagtgggtcatgatttctcctaaattattctcactgatacgcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAGAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
Basic information
species | Glycine max |
transcript | GLYMA16G00590.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 7
----------------------------------------------gttcctacttttctgaatcttatgagatt-gctgtatagtgggtc------atgatttctcctaaattattctcactga----tacgcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAGAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
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gtacaatactcaacagctgaaattgaataaataaataaaatcatggcatcatggcaaagagaaaattaaaggatgagcagtgtcatgtatctcttgagttgcctttatcatgtcaaacttattaaattgcctgtagGGAAACATTGCAAGGTGGGTGAAGAAAGAAGGAGATAAAGTCTCACCTGGTGAAGTTCTTTGTGAAGTAGAGACT
upper sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 3'ss of exon 6
---------------------------------------------gttcctacttttctgaatcttatgagattgctgtatagtgggtcatgattt---ctcctaaattattctcactgatac-----------gcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAGAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
||| || ||| |||| || | ||| | | || | | || | || | || || |||| || | || | |||| ||||||||||| ||| ||||||| ||||| |||| |||| ||||||||||| |||||||| || || ||
gtatctgttacgcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaccgttgctccttatctgtatttcttgaattgcatccatcg-gtgttacacctttaacaccagaagtattacaccttacacttgtattgtctgtagGGGAACATTGCAAGGTGGCTGAAGAAGGAAGGAGATAAGGTCTCACCTGGTGAAGTTCTCTGTGAGGTGGAGACG
upper sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G13930.1 (Arabidopsis thaliana), 3'ss of exon 7
gttcctacttttctgaa--tcttatgagatt----gctgtatagtgggtcatgatttctcctaaattattctcactgatacg-cagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAGAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
| ||| | | | ||||| || | | || || || | || ||| | || ||| ||| || |||||||||||||| || ||| |||||||||||||||||| | | |||||||||||||||| |||||||||||||||
gcatgtacctctgaatacctcttacgaaaattaacatggtttattgttttatcattctactaaagatatct--gttgaaacttcagGGTAACATTGCCAGGTGGCTGAAGAAAGAAGGTGATAAAGTTGCTCCTGGTGAAGTGCTTTGTGAAGTTGAAACT
upper sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G54220.2 (Arabidopsis thaliana), 3'ss of exon 6
--gttcctacttttctgaatctta--tgagattgctgtatagtgggtcatgat-ttctcctaaattattctcactgatacgcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAGAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
| | || | | |||| | | | ||| | || | || |||| ||| | || || || |||||||||| || || ||| |||| ||||||||||||| | | ||||||| ||||| ||||||||||||||||||
gcatggatctttatttacctcttgatcaaaacttatgtccgttttatctttatgttctaataagctttttcca---atttttagGGTAACATCGCCAGGTGGCTGAAAAAAGAAGGTGATAAAGTTGCTCCTGGGGAAGTACTCTGTGAAGTTGAAACT
upper sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 7
gttcctacttttctgaatcttatgagattgctg--tatagtgggtca--tgatttctcctaaattattctcactg--atacgcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAGAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
| | | |||||||| || |||||| | | || | | || ||| | | | | || | | | | ||||||||||||||| || |||||||||||||| ||||||| ||||||||||||||||||||||||||||||||| |||
gcatgtgcctttctgaagct-atgagaatacaaaccatgctcaatttactgttttatgattgaatgttttgtttatcaaatgcagGGTAACATTGCGAGGTGGTTGAAGAAAGAGGGTGATAAAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAGACTMapped 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|209712758|gb|BW681612.1|BW681612EST: CCCCACACCAGGAAATTGGAATGCCTTCTCTCTCACCTACAATGACAGAG GGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAGAATCTCTCCTGGT
genomic: CCCCACACCAGGAAATTGGAATGCCTTCTCTCTCACCTACAATGACAGAGgttcctactt ... tgatacgcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAGAATCTCTCCTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agattgctgtatagtgggtcatgatttctcctaaattattctcactgatacgcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAGAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
ttctcact CT-rich tract
taaattattct 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
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gttcctacttttctgaatcttatgagattgctgtatagtgggtcatgatttctcctaaattattctcactgatacgcagGGTAACATTGCAAGATGGTTGAAGAAAGAAGGTGATAGAATCTCTCCTGGTGAAGTGCTCTGTGAAGTTGAAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG