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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggttatgtattttggtttttatcacattctctagaattttcactatccatattgaaatgttaggcgtataattttatgctaaaagtttgcaatttaagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGA

Basic information

species Glycine max
transcript GLYMA18G46390.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os04g58580.1 (Oryza sativa), 3'ss of exon 7
ggttatgtattttggtttttatcacattctctagaattttcactatccatattgaaatgttaggcgtataattttatgctaaaagtttgcaatttaagttct-caGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGA-
                          | |     | | || || |     | | |  |||||    |        |||  |||  |     | |||  | ||  |||| || || || || || |||||||| || || |||||||| ||||| || ||  | ||||||||||| || |||||||| ||||| |||||||| 
-------------------------gtacaaacaattctttacaaagagcaataatttgttatcattcaggcaccatg--aaacttaactgacttatttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT

upper sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 8
ggttatgtattttggtttttatcacattctctagaattttcactatccatattgaaatgttaggcgtataattttatgctaaaagtttgcaatttaagttct-caGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGA-
              || |  ||    | ||  |      |  || | | || |   |    | |     || | ||||  |        || || |  | || ||||| || || || || || |||||||| || || |||||||| |||||||| ||  | ||||||||||| || || ||||| ||||| |||||||| 
--------------gtataaattgtgtactaaaagtcagtaccttttcttagtaggagaggatggaataaaatctatgggactgaa--acagttgatttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT

upper sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G45790.1 (Arabidopsis thaliana), 3'ss of exon 6
ggttatgtattttggtttttatcacattctctagaattttcactatccatattgaaatgttaggcgtataattttatgctaaaagtttgcaatttaagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGA-
                 |  |  | | | | |  | |||   | ||   |  |  ||| |     |   | | | || | | |  |||    |||||      ||||||| || || || || || |||||  ||| ||||||||||  |||||| ||||||||| | || ||||| ||||| ||||||||||| || || 
----------------gtagaagaaactatatttagtttgttcaatttcttatagaatatattttgagcattgtcattcaacactttt----tttaaa-----agGTTCAAAACATCCGACCAAAGATGGTAGCTGAACTTCGTGAGCGGTTTGCACATCTTAACCTTACTTTCTCAATTGGGGGACAGATAAGCTTCGAT

upper sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv15s0046g03520.t01 (Vitis vinifera), 3'ss of exon 7
---------------------ggttatgtattttggtttttatcacattctctagaattttcactatccatattgaaatgttaggcgtataattttatgctaaaagtttgcaatttaagttc---tcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGA-
                         |     ||    | | |     |  |   |    |  | |     ||||   ||   |  | |  |   | |  | || |     |||||||   ||   |||| ||||||| ||||| ||||| ||||||||||| |||||||||||||||||||| || ||| ||||||| || ||||||||||| ||||| ||||| 
gtataaacttcagatccttcgaagcaaaagattgaactgtcaatttgtgtttgtggcaataaattgattgtatttggat---aaacatgcatcctgaaacaaacaa--cacaatttataatcatatcagATTCACAACATACGTCCGAAGATGGTTTCTGTGCTTCGTGAGAAGTTTGCTCACCTAAACCTGACATTTTCTATTGGAGGACAAATAAGCTTTGAT

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|7284889|gb|AW597376.1|AW597376
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|213618074|gb|DB963707.1|DB963707
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACGATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|213593867|gb|DB981335.1|DB981335
EST:     GGCCGAAATACAAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTTTCGATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|151402864|gb|EV272677.1|EV272677
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|192303883|gb|FG998235.1|FG998235
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|213617059|gb|DB961539.1|DB961539
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACGATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|16348803|gb|BI974398.1|BI974398
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|192298879|gb|FG987624.1|FG987624
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|213592632|gb|DB979423.1|DB979423
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTGGCGATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|22928887|gb|BU546026.1|BU546026
EST:     GGCCGAAATNNTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|192306997|gb|FG999988.1|FG999988
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGCTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|197664690|gb|FD480363.1|FD480363
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACGATATACGCCCGAAAATGGTTTCTGTAC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTAC
EST: gi|13790673|gb|BG653264.1|BG653264
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|31469416|gb|CD411444.1|CD411444
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|192306982|gb|FG999987.1|FG999987
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGCTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|192321031|gb|FK013519.1|FK013519
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|151394726|gb|EV264597.1|EV264597
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|192299912|gb|FG991786.1|FG991786
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|151402943|gb|EV272756.1|EV272756
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|31467953|gb|CD409981.1|CD409981
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
EST: gi|192303884|gb|FG998236.1|FG998236
EST:     GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAA                         GGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC
genomic: GGCCGAAATTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAggttatgtat ... taagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgaaatgttaggcgtataattttatgctaaaagtttgcaatttaagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGA
                           tgctaaa  putative branch site (score: 2)
                                                 ttctc  putative PPT
                 tataattttatgctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttatgtattttggtttttatcacattctctagaattttcactatccatattgaaatgttaggcgtataattttatgctaaaagtttgcaatttaagttctcaGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA