Sequence
atgc intronic sequence ATGC exonic sequence...ggcttatatattatgattgtaatgtaaggattacctgtggtttctttttaaatgttactgaccagacgcaattgtcatgtgctatgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
Basic information
species | Glycine max |
transcript | GLYMA11G05340.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 4
--ggcttata-tattatgattgtaatgtaaggattacctgtggtttctttttaaatgttactgaccagacgcaattgtcatgtgctatgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
| ||||| | | |||| | | || || | |||| || || || | || || || || | ||| || ||||||||| || ||||||||| | || ||||| || ||| ||||||||||| ||||||||||||||||||||||| |||||||||||||||
cagtgttatagcaaatttattggttttagaagactatata-agttttcttatatttgaaaatg--tggatagttttatctgcaaacttattttctttatccagATACTTCAAAGGGCCTGAATTGCTGGTTGACTTCCAAAGTTATGACTACTCTTTAGACATGTGGAGCCTTGGCTGTATGTTTGCTGGAATG
upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 4
ggcttatatattatgattgtaatgtaaggattacctgtggtttctttttaaatgttactgac-cagacgcaattgtcatgtgctatgctt------ttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
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------tgtggttttctt-tgatttctgaaatttttatagtaagatgggagatcctaagaattcagattttttcgtaaggtttgaagttcctttccttgttactcagATACTTTAAGGGGCCAGAACTTCTTGTTGATTTGCAAGATTATGATTATTCTTTGGATATGTGGAGCCTTGGTTGCATGTTTGCGGGAATG
upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 4
ggcttatatattatgattgtaat--gtaaggattacctgtggtttctttttaaatgttactgaccagacgcaattgtcatgtgctatgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
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attttctatagcatagacttgatttgtttgtataaatatcttgcttgctgtataggcaattttctag--gatgttaatatttgcatgttccctgtaatccagATACTTTAAGGGGCCTGAACTTCTTGTTGATTTGCAAGACTATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATG
upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 4
ggcttatatattatgattgtaatgtaaggattacctgtggtttctttttaaatgttactgaccagacgcaattgtc-atgtgctatgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
|| ||| | || | || ||||| | || |||| | |||||| | || |||||||||| || || || || || || || || |||| ||||| || ||||| | |||||||||||||| ||||||||||| |||||||||
-----------------------gtgtggaaaaggcgttgc------ttgaatgtgatc--tcaattccaataatttgtgtgctgtcgcttctcacgtcagATACTTCAAAGGTCCGGAGCTGCTTGTGGACCTGCAGGACTACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATG
upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ28543 (Selaginella moellendorffii), 3'ss of exon 4
ggcttatatattatgattgtaatgtaaggattacctgtggtttctttttaaatgttactgaccagacgcaattgtc-atgtgctatgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
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-----------------------gtgtggaaaaggcgttgc------ttgaatgtgatc--tcaattccaatcatttgtgtgctgttgcttctcacgtcagATACTTCAAAGGTCCGGAGCTGCTTGTGGACCTGCAGGACTACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATGMapped 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|207689746|gb|GD670949.1|GD670949EST: CTGGAAAGGAATATAATGTCCGTGTGGCTTCAAG ATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTC
genomic: CTGGAAAGGAATATAATGTCCGTGTGGCTTCAAGgtactgttct ... tgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTC
EST:
gi|20813341|gb|BQ297819.1|BQ297819EST: GCTGAATTTTATCATCCTGGAAAGGAATATAATGTTCGTGTGGCTTCAAG ATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTC
genomic: GCTGAATTTTATCATCCTGGAAAGGAATATAATGTCCGTGTGGCTTCAAGgtactgttct ... tgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaaatgttactgaccagacgcaattgtcatgtgctatgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
tactgac putative branch site (score: 1)
tgcttttgtttctc putative PPT
ttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggcttatatattatgattgtaatgtaaggattacctgtggtttctttttaaatgttactgaccagacgcaattgtcatgtgctatgcttttgtttctcagATACTTTAAGGGGCCTGAACTTCTAGTTGATTTGCAAGACTATGACTACTCATTAGACATGTGGAGCCTTGGCTGCATGTTTGCTGGAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA