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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatccctaatttcttctgttttcctttttttttttacctttcatttccattcaagttataatctttttctatttgggtgtctaagtttgactctggattctgtttttgattgttgttttgttttttgtttttcctcaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA

Basic information

species Glycine max
transcript GLYMA16G03940.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G03940.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
gttaatccctaatttcttctgttttcctttttttt-------------tttacctttcatttccattcaagtta--taatctttttctatttg-ggtgtctaagtttgactctggattctgtttttgattgttgttttg-------------------ttttttgtttttcctcaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA
|| |    ||  |   || | | ||  ||||||||              |    ||   |||     |   ||   |  | | |||||||| | ||| || |   |  | ||||   | |||| ||| |||||||||||                   |||| |   |||| |    |   ||||||||||| |||||||||||||||||| | || ||||| ||||| ||||| |  ||| | ||||  || || | ||| |
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctga--tgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA

upper sequence: GLYMA16G03940.2 (Glycine max), 3'ss of exon 1
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 1
gttaatccctaatttcttctgttttcctttttttttttacctttcatttccattcaagttataatctttt--tctatttgggtgtctaagtttgactctggattctgtttttgattg-ttgttttgt-tttttgtttttcctcaat--taatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA
                                                         || |  || || |    | ||| ||||    | |||      |||||  | |   ||||  ||| | ||  ||| |  |     |  ||      ||||||||||| |||||||||||||||||| | || ||||| ||||| ||||| | |||  | || | ||| || || || |
---------------------------------------------------------gtgaggattttgtggcgtgtttcggtg----atttttctatgggatttcgatggggattccttgatctgcgtttctactggctgttgatgcctgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA

upper sequence: GLYMA16G03940.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T01 (Zea mays), 3'ss of exon 1
gttaatccctaatttcttctgttttcctttttttttttacctttcatttccattcaagttataatctttttctatttgggtgtctaagtttgactctggattctgtttttgattgttgttttgttttttgtttttcctcaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA
                 |  |  | |      | | ||    |   || | ||||    |   | | | ||||  |||  | | |   |||   |||||   |  || |||   | | | |||      |||| ||  |   |   ||||||||||| |||||||||||||||||| | || ||||| ||||| || || |  ||  | ||| | || ||    || |
----------------gtgaggatgctggacctctcttggtctgttttccaattctgcctg--accgtgttctgcttgctttttt---ttttgatctgg---ccattcttgccggctttcttg------gtttatcggcg--tcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA

upper sequence: GLYMA16G03940.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
gttaatccctaatttcttctgttttcctttttttttttacctttcatttccattcaagttataatctttttctatttgggtgtctaagtttgactctggattctgtttttgattgttgttttgttttttgtttttcctcaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA
                                         | |  |||||| |   |   | | | | ||||  |||  | | |   |||   |||||   |  || |||   | | | |||      |||| ||  |   |   ||||||||||| |||||||||||||||||| | || ||||| ||||| || || |  ||  | ||| | || ||    || |
----------------------------------------gtctgttttccaattctgcc-tgaccgtgttctgcttgctttttt---ttttgatctgg---ccattcttgccggctttcttg------gtttatcggcg--tcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA

upper sequence: GLYMA16G03940.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
gttaatccctaatttcttctgttttcctttttttttttacctttcatttccattcaagttataatctttttctatttgggtgtctaagtttgactctggattctgtttttgattgttgttttgttttttgtttttcctcaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA--------------------
                 |  |  | |      | | ||    |   || | ||||    |   | | | ||||  |||  | | |   |||   |||||   |  || |||   | | | |||      |||| ||  |   |   ||||||||||| |||||||||||||||||| | || ||||| ||||| || || |  ||  | ||| | || ||    || |                    
----------------gtgaggatgctggacctctcttggtctgttttccaattctgcctg--accgtgttctgcttgctttttt---ttttgatctgg---ccattcttgccggctttcttg------gtttatcggcg--tcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA

upper sequence: GLYMA16G03940.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G150867_T01 (Zea mays), 3'ss of exon 1
gttaatccctaatttcttctgttttcctttttttttttacctttcatttccattcaagttataatctttttctatttgggtgtctaagtttgactctggattctgtttttgattg-ttgttttgt-tttttgtttttcctcaat--taatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA
                                                                   |    |  || ||||  |   |||      |||||  | |   ||||  ||| | ||  ||| |  |     |  ||      ||||||||||| |||||||||||||| ||| | || ||||| ||||| ||||| | |||  | || | ||| || || || |
------------------------------------------------------------------gtggcgtgattcggtgatt---ttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA

upper sequence: GLYMA16G03940.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 1
gttaatccctaatttcttctgttttcctttttttttttacctttcatttccattcaagttataatctttttctatttgggtgtctaagtttgactctggattctgtttttgattgttgttttgttttttgtttttcctcaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA
                                              |    ||||  ||       ||     ||||           |||   |  ||||||    ||    ||   || |  |   ||||  | |         ||||||||||| |||||||||||||| ||| | || ||||| ||||| ||||| | |||  | || | ||| || || || |
---------------------------------------------gtgaggattctggtggcgtgattcggtgattttttctataggatttcgatgcggattcc---ttgatctgcgtttctactgcatgttgatgcctg-----cagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA

upper sequence: GLYMA16G03940.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 1
gttaatccctaatttcttctgttttcctttttttttttacctttcatttccattcaagttataat--ctttttctatttgggtgtctaagtttgactctggattctgtttttgattgttgt-tttgtt--ttttgtttttcctcaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA
                                                     |   ||| | ||  |||||  | || |  |   |  | ||   |  ||| || |    |  ||||||| | ||    ||      |   | | |   |||||||||||||||||||||||| |||||| | ||||||||||||   || || |||||| | || ||||||||   |||||
--------------------------------------------------ggattgtgttgtgattacttttcttgttcgaattggtgcggtt---tggggaatcggcaagttgttgttgtatctgacgattcaagaatgtgtgattgggtagGATGATGAGTGACTACAAGGTCGAGATGGTGAATGATGGAATGAGCGAATTCTATGTGGAGTTTCATGGACCGCGTGAGA

upper sequence: GLYMA16G03940.2 (Glycine max), 3'ss of exon 1
lower sequence: EFJ23672 (Selaginella moellendorffii), 3'ss of exon 1
gttaatccctaatttcttctgttttcctttttttttttacctttcatttccattcaagttataatctttttctatttgggtgtctaagtttgactctggattctgtttttgattgttgttttgttttttgtttttcctcaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA
|| | || |   |    ||   ||||  ||  || ||  |  | || |  |  | ||     || || | | | || |     ||   ||   |||||    ||  ||   |||| |  ||  ||||   |       |  ||   |||||||||||||||||||||||||||||| | || ||||| ||| | |||||| ||||| | |||||||||||    || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggctatgaaa----aacctctctttcttcg-----ctttcttcctctctg----ctaattc--attgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

upper sequence: GLYMA16G03940.2 (Glycine max), 3'ss of exon 1
lower sequence: EFJ34378 (Selaginella moellendorffii), 3'ss of exon 1
gttaatccctaatttcttctgttttcctttttttttttacctttcatttccattcaagttataatctttttctatttgggtgtctaagtttgactctggattctgtttttgattgttgttttgttttttgtttttcctcaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA
|| | || |   |    ||   ||||  ||  || ||  |      | |||| |  |  | |  |  ||  || | |   | |||     | | ||       || || |     |  ||||| ||    ||  ||     ||   |||||||||||||||||||||||||||||| | || ||||| ||| | |||||| ||||| | |||||||||||    || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgc------tctccagtggacctctctttcttcgctttcttcctctctg---ctaattca-----ttgcttct-----tctttttgcttcccattcctc-----tttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

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|19346632|gb|BM891512.1|BM891512
EST:     GTCTTCTCCAAGCAAGCGGCGAGAAATGGACTTGATGAAACT                         GATGATGACTGACTACAAGGTGGAGATGATTAATGATGGAATGCAATAGTT
genomic: GTCTTCTCCAAGCAAGCGGCGAGAAATGGACTTGATGAAACTgttaatccct ... caattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTT
EST: gi|7233955|gb|AW569297.1|AW569297
EST:     TTCTCCAAGCAAGCGGCGAGAAATGGACTTGATGAAACT                         GATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTT
genomic: TTCTCCAAGCAAGCGGCGAGAAATGGACTTGATGAAACTgttaatccct ... caattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctggattctgtttttgattgttgttttgttttttgtttttcctcaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA
             ttttgat  putative branch site (score: 4)
                   ttgttgttttgttttt  CT-rich tract
                         ttttgttttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatccctaatttcttctgttttcctttttttttttacctttcatttccattcaagttataatctttttctatttgggtgtctaagtttgactctggattctgtttttgattgttgttttgttttttgtttttcctcaattaatagGATGATGAGTGACTACAAGGTGGAGATGATTAATGATGGAATGCAAGAGTTTTATGTGCACTTCCATGGACCCAATGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA