Sequence
atgc intronic sequence ATGC exonic sequence...tgttttaataatcttgttatttatttttcaagcattgcttatcattttattactctgggtaaaaagtaagctttctttctgtttttaattttttgatcagATTCATTCTTGACAAGAAAATTGGTATTGGACAACCCAAGCGGATAGAGAATGCAAAGATACTGGTGGCAAACACTGCCATGGACACAGACAAAGTGAAG
Basic information
species | Glycine max |
transcript | GLYMA11G19220.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g42220.2 (Oryza sativa), 3'ss of exon 7
tgttttaataatcttgttatttatttttcaagcattgcttatcattttattactctgggtaaaaagtaagctttctttctgtttttaattttttgat---cagATTCATTCTTGACAAGAAAATTGGTATTGGACAACCCAAGCGGATAGAGAATGCAAAGATACTGGTGGCAAACACTGCCATGGACACAGACAAAGTGAAG
| | || | | || | || || | || | | || || | | | | || ||| ||| || | ||| |||||||||||||||||||||||| |||||||||| ||| | || |||||||| || || | || |||||||| || ||||||||||||||||| |||
-cactgagcaaatacggagtgtactagg-aaacactatac-ccaactgacaaccatgattctgattctgctgtccgtttaacgttttggtttctgttttgcagTTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCAAAGAGAATTGAGAATGCCAAAATTTTAGTTGCAAACACAGCTATGGACACAGACAAAGTAAAG
upper sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g48290.1 (Oryza sativa), 3'ss of exon 8
--tgttttaataatcttgttatttatttttcaagcatt-gcttatcattttattactctgggtaaaaagtaagctttctttctgtttttaattttttgatcagATTCATTCTTGACAAGAAAATTGGTATTGGACAACCCAAGCGGATAGAGAATGCAAAGATACTGGTGGCAAACACTGCCATGGACACAGACAAAGTGAAG
|| | |||| | ||| | || ||| || |||| | ||| | || || | | ||||| | ||||| || |||||||| ||||||||||| ||| |||| ||||| ||| |||| || || || ||||| |||| ||||| ||||| |||||||| |||||||| |||
gaaattatgtaaatcatcatatgttggaagcagccatgagcagatcaaactgaagtcctgctcttgaggtg-gcaatttcatgattttttttcttttg--tagGTTCATTCTAGACAAGAAAATCGGTCTTGGCCAACCGAAGAGGATTGAAAACGCCAAGATTTTGGTTGCAAATACTGCTATGGACACCGACAAAGTTAAG
upper sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 9
lower sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 16
tgttttaataatcttgttatttatttttcaagcattgcttatcattttattactctgggtaaaaagtaa----gctttctttctgtttttaattttttgat-cagATTCATTCTTGACAAGAAAATTGGTATTGGACAACCCAAGCGGATAGAGAATGCAAAGATACTGGTGGCAAACACTGCCATGGACACAGACAAAGTGAAG
| | | | ||| ||||| | | ||| ||| | || | ||| || | ||| | | | | ||||| | | ||| || || || || ||||||||||||||||||||||| ||||| || |||||||| || |||||||| || || |||| ||||||||||| ||||||||||| ||||| |||
--ctgtgagtacctt-ttattgagtgttcttgca--ggcatctatgtaattgttcccaacagaaaatgacactgatatctttttttatttgcttcttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG
upper sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G058276_T01 (Zea mays), 3'ss of exon 7
tgttttaataatcttgttatttatttttcaagcat-tgcttatcattttattactctgggtaaaa--agtaagctttctttctgtttttaattttttgatcagATTCATTCTTGACAAGAAAATTGGTATTGGACAACCCAAGCGGATAGAGAATGCAAAGATACTGGTGGCAAACACTGCCATGGACACAGACAAAGTGAAG
| ||| | | | | | | || |||| | || ||| || | | || ||| ||| | | || || | | ||||||||||||||||||||||||||| || || || || |||||||| |||||||| || || |||| ||||||||||| ||||||||||| ||||| |||
---gagtacaatttattgagtgttcatgcatgcatctatgtaatgtttcccaacagaaaatggtcctaatatcttttttttatttgcttgtttctatttgcagATTCATTCTTGACAAGAAAATTGGCATCGGGCAGCCAAAGCGGATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG
upper sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 8
--tgttttaataatcttgttatttatttttcaagcattgcttatcattttattactctgggtaaaa-agtaagctttctttctgtttttaattttttgatc--agATTCATTCTTGACAAGAAAATTGGTATTGGACAACCCAAGCGGATAGAGAATGCAAAGATACTGGTGGCAAACACTGCCATGGACACAGACAAAGTGAAG
| || ||| || | | | || | | || || | || ||| | |||| | || | || || || | | || || || ||||||||||||||||| || ||||| || || ||||| |||||||||||||| || | || || || ||||| ||||| || || |||||||||
ggaatgttgatagtcatcatgtcatcttgttgtgttgtgtttcttcttctatc-----gagtaatatggtctcatgtcacctcaacttaaaatctatgcctgtagGTTTATTCTTGACAAGAAAATAGGAATTGGGCAGCCTAAGCGCATAGAGAATGCAAATATCTTAGTAGCTAATACTGCTATGGATACCGATAAAGTGAAG
upper sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 9
tgttttaataatcttgttatttatttttcaagcattgcttatcattttattactctgggtaaaaagtaagctttctttct------gtttttaattttttgatcagATTCATTCTTGACAAGAAAATTGGTATTGGACAACCCAAGCGGATAGAGAATGCAAAGATACTGGTGGCAAACACTGCCATGGACACAGACAAAGTGAAG
|| || || || | | | | || | || ||| | | || | ||||| ||| ||| | | | | |||| || || || |||||||||||||| || || ||||| ||||| || || ||||||||||||||||| |||||||||| ||||| |||||||| || ||||| |||
cattcta-tattccaactgtcttctcttt-----tcaattgtcaaacacatccgatgcaaattcagtaaattttttttgttaattggaatcttgttttctgcatagGTTTATTCTTGACAAGAAGATAGGCATTGGTCAACCAAAACGCATAGAGAATGCAAAGATTTTGGTGGCAAATACTGCAATGGACACCGATAAAGTCAAGMapped 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|254325804|gb|GR838685.1|GR838685EST: ATTATAAAGAAACCTGGAGGCTCATTAATGGATTCATTCTTAGATGAAGG ATTCATTCTTGACA-GAAAATTGGTATTGGGACACCCCA
genomic: ATTATAAAGAAACCTGGAGGCTCATTAATGGATTCATTCTTAGATGAAGGgtaatattgc ... ttttgatcagATTCATTCTTGACAAGAAAATTGGTATTGG-ACAACCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttattactctgggtaaaaagtaagctttctttctgtttttaattttttgatcagATTCATTCTTGACAAGAAAATTGGTATTGGACAACCCAAGCGGATAGAGAATGCAAAGATACTGGTGGCAAACACTGCCATGGACACAGACAAAGTGAAG
ttttaat putative branch site (score: 3)
ctttctttctgttttt CT-rich tract
tttctttctgttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttttaataatcttgttatttatttttcaagcattgcttatcattttattactctgggtaaaaagtaagctttctttctgtttttaattttttgatcagATTCATTCTTGACAAGAAAATTGGTATTGGACAACCCAAGCGGATAGAGAATGCAAAGATACTGGTGGCAAACACTGCCATGGACACAGACAAAGTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - ttcaagc
- - - - - - - - - - - - - - - - - -tgcttat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtaaaaa