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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggattctaaattgtcccccccccccctctcttatgtttttggttaaatgaatatctgatggcacttactagtgaagcactgtaaacattttaacttccactgttgcagCATGATGTTGTTGCATCATATTTAGATAGTGGAGGGCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA

Basic information

species Glycine max
transcript GLYMA07G03890.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 14
--------gtgaggattctaaattgtcccccccccccctctcttatgtttttggttaaatgaatatctgatggcacttacta----gtgaagcactgtaaacattttaacttccactgttgcagCATGATGTTGTTGCATCATATTTAGATAGTGGAGGGCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
         ||     |||||||  ||           ||| || |  | |||  |   | | |   |||  |  |||  |      ||       || |   || ||| ||    |  | |||   ||||| ||||| || ||| ||||   ||||   ||||| |||||| |||| ||||||||||| |||||||| ||||||||  | ||||| || ||  
gtaagttattgtattatctaaatgttcattatgttatttcttttctcctcttgaatgtgttattgcgtgaaagttctttttttaccatggcatgaagttatgtttgtaatttgtgttcctacagAGAGATGTCGTTGCGTCTTATCTAGAATCTGGAAAACCTGTGGATGAGGAAGGCGTTGAAGATGCTTTTGAGCTGCTTCATGAGGTTAATGAGCGAGTGC

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 5
gtgaggattctaaattgtcccccccccccctctcttatgtttttggttaaatgaatatctgatggcacttactagtgaagcactgtaaacattttaacttccactgttgcagCATGATGTTGTTGCATCATATTTAGATAGTGGAGGGCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
               |        |  |  | | ||   | | | ||| |||||        |  ||  ||||  ||| | |     ||||    || ||  ||  || |||   ||||| ||| | ||  |||| ||| | || ||  | || |  ||| ||||||| |||||||||||||| || |||||||| || ||||||||  || 
--------------gtaagtttttctgcattttgttggctctgtagttcaatgat------gtaacatctact--tgatgtaactataacacaacaa-ttatacc-ttccagAGGGATGTAGTTTCTTCTCATTTGGATGGAGGGGGTTCAGTTGGCGAGGAAGGTGTGGAAGATGCCTTTGAACTACTTCATGAGATCAATGAACGCATCC

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 14
---------------------------------gtgaggattctaaattgtcccccccccccctctcttatgtttttggttaaatgaatatctgatggcacttactagtgaa---gcactgta--aacattttaacttccact---gttgcagCATGATGTTGTTGCATCATATTTAGATAGTGGAGGGCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
                                   |  ||   |  | |  |  || |     | | |  | |||   || |||| || |    ||     || || || ||   | | ||||  || |    |  ||||  |    ||| ||   ||||| ||| ||||  |||||||  | || ||  | |  | |||| ||||||| |||||||||||||| || |||||||| || |||||||||||| 
gtgagttctgtcactgtcttaattgcctatgttcagttgacctttcagttacatccactattttttgtcctttttaatgtcaaattaagaagaaattattttt-ctggtcaaattgaaatgtattaatacaaaagtttccttttatcttgtagAGGGATGTAGTTTCATCTCATTTAGACGGAGGGGGTTCAGCTGCTGAGGAAGGTGTGGAAGATGCCTTTGAACTGCTTCATGAGATCAATGAACGTGTCC

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 15
------------gtgaggattctaaattgtcccccccccccctctcttatgtttttggttaaatgaatatctgatg--gcacttactagtgaagcactgtaaacatt-ttaacttccactgttgcagCATGATG---------------TTGTTGCATCATATTTAGATAGTGGAGGGCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
                  ||| || ||          | |  | | ||||  |  |||||||    ||||   ||   |||  |   | ||     |  |    ||| || |||  | |   |  | | ||||                | ||| | ||  || ||||| | || |   | || |  ||| ||||||||||||||||||||||  | |||||||| || |||||||||||| 
gtgagttaattttcacatattgtagat-actgtagatcacagttttttattgtgctggttaagcacatattgtattctgcaactgacaatggtatgccttgtctattatttactaacgcaactctaacttgataacatctagAGGGATCTAGTTTCTTCTCATCTAGATGGAGGGGCATCAGTTGGCGAGGAAGGTGTTGAAGATGCCTTTGAATTGCTTCATGAGATAAATGAACGTGTCC

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 14
-------------------------------gtgaggattctaaattgtcccccccccccctctcttatgtttttg--gttaaatgaatatctgatggcacttactagtgaagca---ctgta--aacattttaacttccac---tgttgcagCATGATGTTGTTGCATCATATTTAGATAGTGGAGGGCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
                                ||   | || |  ||       |  || ||   || ||| |||   || |||| || |    ||     || || || ||       ||||  ||||    |  ||||     | ||| ||   ||||| ||| ||||  |||| ||||| || ||  | |  | |||| ||||||| |||||||||||||| || |||||||| || || ||||||||| 
gtgagttctgtcattaccttattaattgcctatgttcagtcgacctttctgttacatccactgatttgtgtcttttatgtcaaattaagaagcaatcattttttctggtcaaatggacatgtactaacacaaaagtttccttttatcttgtagAGGGATGTAGTTTCATCTCATTTGGATAGAGGGGGTTCAGCTGGTGAGGAAGGTGTGGAAGATGCCTTTGAACTGCTTCATGAGATCAACGAACGTGTCC

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S61_1V6.1 (Physcomitrella patens), 3'ss of exon 14
------------gtgaggattctaaattgtcccc--cccccccctctcttatgtttttggttaaatgaatatctgat-ggcacttactag-tgaagcactgtaaacattttaacttccactg--ttgcagCATGATGTTGTTGCATCATATTTAGATAGTGGAGGGCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
             | |   |||||   | ||      |     || || ||      |   ||  ||   || | ||   ||||   | | || |   | || |||   | |   |   |||  || |||   || |||||  |||||||||| ||||||||   |||||| || |||||||||||||| ||||| |||||  | ||||||||| |    || |||||  
gtaagtatcaatatcatatttctatgctctctttaatctttttctgtcctacaccaatttgtatttgctcatgtcattaacactctttgggtggaattcagtcaactcatgattgtgtgctgcctttcagAGGGACGTTGTAACATCATATTTGGATAGTGGCAAGCCTGTGGACGAGCAAGGTGTTGAGGATGCGTTTGAATTACTTCATGAAGTATCGGAGCGTGTTC

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|254341657|gb|GR852794.1|GR852794
EST:     ATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT                         CATGATGTTGTTGCATCATATTTAGATAGTGGAGGGCCTGTAGATGAGCAA
genomic: ATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAATgtgaggattc ... actgttgcagCATGATGTTGTTGCATCATATTTAGATAGTGGAGGGCCTGTAGATGAGCAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgatggcacttactagtgaagcactgtaaacattttaacttccactgttgcagCATGATGTTGTTGCATCATATTTAGATAGTGGAGGGCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA
                                  ttttaac  putative branch site (score: 2)
                                        cttccact  CT-rich tract
                            taaacattttaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggattctaaattgtcccccccccccctctcttatgtttttggttaaatgaatatctgatggcacttactagtgaagcactgtaaacattttaacttccactgttgcagCATGATGTTGTTGCATCATATTTAGATAGTGGAGGGCCTGTAGATGAGCAAGGTGTTGAAGATGCCTTTGAGCTCCTTCATGAAATGAATGAACGTGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG