Sequence
atgc intronic sequence ATGC exonic sequencegtagtaacctcaacatctctcaaataattttaaaaaataattgttgattacatgtcttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttgtattcttggtgttttggattgttgttgtattgattatgtactatatggactctcactgtccttattatgcccccccttataattagGAGGATATGGAACCATGGAAGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG
Basic information
species | Glycine max |
transcript | GLYMA04G05550.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g51210.2 (Oryza sativa), 3'ss of exon 3
gtagtaacctcaacatctctcaaataattttaaaaaataattgttgattacatgtcttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttgtattcttggtgtt-ttggattgttgttgtattgattatgtactata-tggactctcactgtccttattatgcccccccttataattagGAGGATATGGAACCATGGAAGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG
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---------------------------------------------------------------------------------------gtattacactcagttctacatgttttcttgatactatttgaacgggctaatatttcaaac-caccatgcttaattactgacaacttttttgtggac---------aatagGAGGGTATGGAACAATGGAGGAGTTGTTAGAGATGATAACTTGGTCACAACTTGGAATTCATGACAAACCA
upper sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g46360.2 (Oryza sativa), 3'ss of exon 4
gtagtaacctcaacatctctcaaataattttaaaaaataattgttgattacatgtcttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttgtattcttggtgttttggattgttgttgtattgattatgtactatatggactctcactgtccttattatgcccccccttataattagGAGGATATGGAACCATGGAAGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG
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------------------------------------gtaattgataattcca------atatatgtgagatggactga---cgatctgaaatgttcagtaccttctttctaacatca-tctatcacactagta----attgataattca--------aatgtaact-tggttattga--------tttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA
upper sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g46360.3 (Oryza sativa), 3'ss of exon 4
gtagtaacctcaacatctctcaaataattttaaaaaataattgttgattacatgtcttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttgtattcttggtgttttggattgttgttgtattgattatgtactatatggactctcactgtccttattatgcccccccttataattagGAGGATATGGAACCATGGAAGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG-----------------------------
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------------------------------------gtaattgataattcca------atatatgtgagatggactga---cgatctgaaatgttcagtaccttctttctaacatca-tctatcacactagta----attgataattca--------aatgtaact-tggttattga--------tttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAGTAAGCATAATTGAGATATTTGATACTAG
upper sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 4
gtagtaacctcaacatctctcaaataattttaaaaaataattgttgattacatgtcttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttgtattcttggtgttttggattgttgttgtattgattatgtactatatggactctcactgtccttattatgcccccccttataattagGAGGATATGGAACCATGGAAGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG
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--------------------------------------------------------------------------------------------gtgagaaaacgctttaaaact----gaatcctagctaattgttaaagttgaaagttttggtatcaaaaactacggggttt----------------tgttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG
upper sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g01040.t01 (Vitis vinifera), 3'ss of exon 4
gtagtaacctcaacatctctcaaataattttaaaaaataattgttgattacatgtcttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttgtattcttggtgttttggattgttgttgtattgattatgtactatatggactctcactgtccttatt-atgcccccccttataattagGAGGATATGGAACCATGGAAGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG
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-------------------------------------------------------------------------------------------------gtaactaccttggacattatattccttaaag-acaaaagta--gatcatcttctatat--actcaggatactattgtttgagtttcaaattgttgt-agGAGGATATGGAACCATGGAAGAGCTGCTGGAGATGATTACATGGTCGCAACTGGGAATTCATAAAAAACCAMapped 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|209721045|gb|BW666302.1|BW666302EST: GCGTAAGGCTGCAATGGCACAAGAAGCTGATGCATTTGTTGCTCTCCCTG GAGGATATGGAACCATGGAAGAGCTGTTGGAGATGATAACTTGGGCCCAAC
genomic: GCGTAAGGCTGCAATGGCACAAGAAGCTGATGCATTTGTTGCTCTCCCTGgtagtaacct ... ttataattagGAGGATATGGAACCATGGAAGAGCTGTTGGAGATGATAACTTGGGCCCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattatgtactatatggactctcactgtccttattatgcccccccttataattagGAGGATATGGAACCATGGAAGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG
ctctcac putative branch site (score: 3)
ttatgccccccctt putative PPT
ttataatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtaacctcaacatctctcaaataattttaaaaaataattgttgattacatgtcttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttgtattcttggtgttttggattgttgttgtattgattatgtactatatggactctcactgtccttattatgcccccccttataattagGAGGATATGGAACCATGGAAGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG