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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatttattctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG

Basic information

species Glycine max
transcript GLYMA12G06990.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 5
--------tatatttattctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG
        | ||||   | ||   || |  |  |||  |   |  || | |   | ||   | | |||| |      ||| |||   | ||   ||| || |  |||||| || |||||||| || || || || |||||||||||||| ||||||||| ||||||| || ||
gtacagtctctattatatatataactctgttaagtccaactattcaaatacaaatcttgttcatgtcct-gttctgatatttaaatggatgtataatcatgt--acagACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAG

upper sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 4
tatatttattctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG
    | |  |  |  ||||| |  ||  |  |       ||    |||   || || ||||   || | |        |||| |  | |   | | |||||| || ||||||||||| |||||||| ||||||||||| || ||||| ||| ||||||| || ||
---gtatgctagatctctgttacatgagaggt------ggtatattttcatagtttttcct---gatattg------gtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 11
tatatttattctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG
      ||| |||  ||| |  ||  | | |  | | |  ||    ||   || || ||||   || | |        |||| |  | |   | | |||||| || ||||||||||| |||||||| ||||||||||| || ||||| ||| ||||||| || ||
-----gtatgctagatctctgctgcatgagaggtggtatatt----ttcatagtttttcct---gatattg------gtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 5
tatatttattctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacac-tatctaatatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG
      ||| ||| |||| |  | ||| | |    | | |||  ||||   || || |||| |     | |   |    |||| | || |   | | |||||| || ||||||||||| |||||||| ||||||||||| || ||||| ||| ||||||| || ||
-----gtatactagttctctgctctgtgagagacagtacgtt--gtttaatagtttttcctggtatttcatgattttggtgtttgtaatttcctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG

upper sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 5
tatatttattctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG
      ||| |||  ||| |  ||  | | |  | | |  ||    ||   || || ||||   || | |        |||| |    |   | | |||||| || ||||||||||| |||||||| ||||||||||| || ||||| ||| ||||||| || ||
-----gtatgctagatctctgctgcatgagaggtggtatatt----ttcatagtttttcct---gatattg------gtgtttgtggttgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 6
tatatttattctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG
      ||| |||  ||| |  ||  | | |  | | |  ||    ||   || || ||||   || | |        |||| |  | |   | | |||||| || ||||||||||| |||||||| ||||||||||| || ||||| ||| ||||||| || ||
-----gtatgctagatctctgctgcatgagaggtggtatatt----ttcatagtttttcct---gatattg------gtgtttgtgattgtatgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTGGAGCTAG

upper sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 2
tatatttattctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG
      ||| |||| ||| |  ||  | | |  | | |  ||    ||   || || || |   || | |        |||| |  | |   | | |||||| || ||||||||||| |||||||| ||||||||||| || ||||| ||| ||||| | || ||
-----gtatgctacatctctgctgcatgagaggtggtatatt----ttcatagtttttctt---gatattg------gtgtttgtgattgtctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTAGGACTTGCAAAGAGAGTTAGAGCTAG

upper sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
tatatttattctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaata-atttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG
                  ||   |||| | || | || |  |     | ||| |||    |    | | |   || |   |     ||||  ||| | |||||||| ||||| ||||||||||||||||| |||||||| || ||||||||||| ||||| |||||
------------------gtt-cgtgtga-atatagatatattctcatatcaccttcatataatcagaatcgttagttactgatctaatatgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG

upper sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 4
tatatttattctacttctgtcatgtgtcatatcttg-aaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaataattt--ttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG-----------------------------------
    ||| ||  ||||| || |    ||| | || | ||| | ||   |   |  || |   |||   |  |||  ||||  |    |    | |  |  ||||| ||||| |||||||||||||| ||||| |||||| | || || || ||||||||||| |||||                                   
---gtttgttaaacttc-gtta---atcaaaactcgcaaaatgctagctgatatatt-tttatgacttatgatcatatatccttttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG

upper sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 5
tatatttat-tctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaa----tatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG
    || |  ||||  | | |  |||   || ||     |||  | |      |   ||  |||||| | | ||| |    | |  |      | | ||| |||||||||||| ||||| || |||||||||||||| ||||| || |||||||| |||||||| |||||
----ttgacgtctagattttttgtgttcaatgtcagtgcagtcatttgaacttgtgaattattgaga-attgtctgacttttttacttaactgtcactttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG

upper sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
--tatatttattctacttct--gtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG
  ||||| |||   | | ||    | | |||    |   || |  | ||  |||||| ||    |||       || |     ||| | || |   |||| ||||| || |||||||||||||||||||| || ||||||||||| || || || |||||||| |||||
tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttg----gtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG

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|298196598|gb|HO041341.1|HO041341
EST:     ATCTTGCGTGCCCTGCATCTCCTATTTTCTACAAATATAATCCCGTGAAG                         ACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAG
genomic: ATCTTGCGTGCCCTGCATCTCCTATTTTCTACAAATATAATCCCGTGAAGgtatagtttt ... atttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAG
EST: gi|16277140|gb|BI942224.1|BI942224
EST:     ATCTTGCGTGCCCTGCATCTCCTATTTTCTACAAATATAATCCCGTGAAG                         ACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAG
genomic: ATCTTGCGTGCCCTGCATCTCCTATTTTCTACAAATATAATCCCGTGAAGgtatagtttt ... atttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAG
EST: gi|298196896|gb|HO041639.1|HO041639
EST:     ATCTTGCGTGCCCTGCATCTCCTATTTTCTACAAATATAATCCCGTGAAG                         ACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAG
genomic: ATCTTGCGTGCCCTGCATCTCCTATTTTCTACAAATATAATCCCGTGAAGgtatagtttt ... atttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcagcttatccttgagacactatctaatatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG
                         atctaat  putative branch site (score: 3)
                                              tttttac  putative PPT
                                        aaataatttttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatttattctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG

- - - - - - - ttctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttggg