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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgctcttcaacttcgatttcgcactcctttggtcaaccttcttgacatttgttcttttttattattattattcttatgttgttgtcgtgtgttgtgtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC

Basic information

species Glycine max
transcript GLYMA10G00490.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 1
gttcgctcttcaacttcg----atttcgcactcctttggtcaaccttctt------gacat------ttgttcttttttattattatta-ttcttatgttgttgtcgtgtgttgtgt-aattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC
|| || ||| |  |  ||    |  |     | |||    || | ||| |      || ||      |||  | |||| ||   ||  | ||  | || | |  ||   || ||  | ||   ||||| || || |||||||||||    ||||| |      |||| || || ||||| ||||||||| | ||||||||||| ||||||||| |||||||||| |
gtacgttctccgccgccggagtaccttttttttcttcttacagctttcgtttctcagatataacagcttgagcgttttgatctctaacaatttctgtggtttcttctattggtggatgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTCGACCACTTCGAGAGAAAGCGCAAGAAGGAGGCGCGTGAAGTTCACAAGC

upper sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 1
gttcgc--tcttcaacttcgatttcgcactcctttggtcaaccttcttgacatttgttcttttttattattattattcttatgttgttgtcgtgtgttgtgta--attgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC
||| |    | |    ||| |      | | |  | |   |  |  ||   |     ||  |  | || | ||| |  || ||| |||||  ||| ||||      || ||||||||||| ||||||||||| | ||| || |    | ||||||| || |  || || |||||||| ||||||||||||||||| ||| |||||||||| |
gttagtatccgtttgtttccaaggaaaatttccctagaagatttatttccaacaaagtcagtgat-ttctgattgtattt-tgtggttgtt-tgtattgtcctctgtttcagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGC

upper sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S136_220V6.1 (Physcomitrella patens), 3'ss of exon 1
gttcgctcttcaacttcgatttcgcactcctttggtcaaccttct-tgacatttgttcttttttattattattattcttatgttgttgtcgtgtgtt---gtgtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC
        || ||    | | | |   |  |||||| |   ||   ||     | |      ||| | ||  ||||||  |||| ||    | ||||         |  |||||||| || ||| | || ||    ||  | |      |||| ||||| |  ||| |||||||  |||||||||||||||| |||||| ||||||| ||||
-------tttgaa----ggtgtagagtttgtttggttagttttgaatggtgagtttgtaaacttacttttggtattct-gtgttatttgtttttgtttccactgggtaacagCCGCAGGGAGATCATATTGACTTGCATCGCAAGCGTCATGGGTACCGACCGGATTACTTCGAAAGGAAGCGCAAGAAAGATGCGCGTGAAGTTCATAAAC

Mapped 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|26059399|gb|CA802313.1|CA802313
EST:     TGTTCTGAAACCACTCCCGCCTCCTC-TAAAGGTG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
genomic: TGTTCTGAAACCACTCCCGCCTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|11413156|gb|BF425167.1|BF425167
EST:     GCCTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
genomic: GCCTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|20498024|gb|BQ272954.1|BQ272954
EST:     AAACCACTCCCGCCTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
genomic: AAACCACTCCCGCCTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|15813104|gb|BI785379.1|BI785379
EST:     CTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
genomic: CTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|298179957|gb|HO025172.1|HO025172
EST:     CTCTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
genomic: CTCTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|5606189|gb|AI900287.1|AI900287
EST:     TCTGAAACCACTCCCGCCTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
genomic: TCTGAAACCACTCCCGCCTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|298178157|gb|HO027540.1|HO027540
EST:     CTCTTCCTCTTTCTCTGTTCTAAAACCACTCCCGCCTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
genomic: CTCTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|209725840|gb|BW654703.1|BW654703
EST:     CTCTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
genomic: CTCTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|120530814|gb|EH258947.1|EH258947
EST:     CTCTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
genomic: CTCTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|298182139|gb|HO026314.1|HO026314
EST:     CTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAAACTATGGCTACCGTCTC
genomic: CTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|298189817|gb|HO038220.1|HO038220
EST:     CTCTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
genomic: CTCTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|192329667|gb|FK022933.1|FK022933
EST:     CTCTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
genomic: CTCTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|192333080|gb|FK026409.1|FK026409
EST:     CTCTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
genomic: CTCTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|120530581|gb|EH258714.1|EH258714
EST:     CTCTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATG                         CCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC
genomic: CTCTTCCTCTTTCTCTGTTCTGAAACCACTCCCGCCTCGTCGTCACCATGgttcgctctt ... gtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcttttttattattattattcttatgttgttgtcgtgtgttgtgtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC
     tttttattattattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgctcttcaacttcgatttcgcactcctttggtcaaccttcttgacatttgttcttttttattattattattcttatgttgttgtcgtgtgttgtgtaattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG