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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcttatccaatttgtctctgaatcttgtcaatgtaaggagacaatattgtggccaatgcaatcaaatatgtatcctgactatgatgtcttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAG

Basic information

species Glycine max
transcript GLYMA11G01300.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G01300.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G016106_T01 (Zea mays), 3'ss of exon 3
--tggcttatccaatttg-tctctgaatcttgtcaatgtaaggagacaatattgtggccaatgcaatcaaatatgtatcctg--actat--gatgtcttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAG
  | |  | || ||| || |||    ||   ||   ||        || |  ||||     | || |  | | |    | ||  ||| |  ||     |  ||||||||||||||||||| ||||| || || ||| | || |||||||| ||||||||||||||||||  ||| || ||| ||| ||| |||
gtttgtatctctaatatgctctgcagattcagttgctgc-------cacttatgtgcatgtttcagttgactgttccccttgttacttttggacaaacttctttcagGAAAGTATGTTGGGAATCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGCAAAGACAAAAG

upper sequence: GLYMA11G01300.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G068255_T01 (Zea mays), 3'ss of exon 3
--tggcttatccaatttgt-ctctgaatcttgtcaatg-taaggagacaatattgtggccaatgcaatcaaatatgtatcctg--actat--gatgtcttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAG
  | |  | || ||| ||| ||    ||   ||   ||    |  |  | |  ||||   | |    |  | | |  | | ||  ||| |   |   | |  ||||||||||||||||||| || || || || ||| | || |||||||| ||||||||||||||||||  ||| || ||||||| ||| |||
gtttgtatctctaatatgttctgcagattcagttgctggcttgctgctacttatgtgcatattttggttgagtgttcaccttgttacttttgaacaacattctttcagGAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG

upper sequence: GLYMA11G01300.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G04500.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------tggcttatcc----aatttgtctc-tgaatcttgtcaa----tgtaaggagacaatatt--gtggccaatgcaatcaaatatgt--atcctgacta-tgatgtcttggt----ttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAG
                                   ||  | |||     |  |  ||||     | ||||||     ||| |   ||   | ||   |   || ||   |  || ||    ||   | | | |||| || |         |||| ||||||||||||||||| |||||||||||||| |||||||  ||||| ||||| |||||| | || ||    |||| ||| |||
gtaagcaccttgtttttagtttctgtttgatgtgttgcttcatcttgatatctcatctcactgtttttgtcagaacttgttatatgattctgttctataatcactgtcgttgaacattctgatttggtccactgatttcatatgaatacacagGTAAGTATGTTGGAAATCGTCCGATAAAACTACGAAAGAGTAGCTGGAAAGAGAGAACAGATCAGGAGGCTGCTGAAAGACAAAAG

upper sequence: GLYMA11G01300.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0018g01710.t01 (Vitis vinifera), 3'ss of exon 4
tggcttatc-caatttgtctctgaatcttgtcaa-tgtaaggagacaatattgtggccaatgcaatcaaatatgtatcctgactatgatgtcttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAG
  | ||||      |  |        || || || | | || |   |  |  ||     ||  |||    ||  |||  ||| |   || ||    ||||||| ||||||||||||||| |||| || |||||||| ||||| || ||||||||||||||||||| ||||||  |||||| ||| |||
-aggttatggtggctcattataatgactagtaaagtttgagcattgagaaaagttttggatataatggcttaaatatgttgatttaaatctca-attttcagGCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAG

upper sequence: GLYMA11G01300.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0036g00630.t01 (Vitis vinifera), 3'ss of exon 4
tggcttatccaatttgtctctgaatcttgtcaatgtaaggagacaatattgtgg-----ccaatgcaatcaaatatgtatcctgactatgatgtcttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAG
      || |     ||        |||   |||   | |    ||| ||| |      |   |  ||| |  || ||||  ||| |   || ||    |||||||||| |||||||||||| |||| || |||||||| ||||| || |||| |||||||||||||| ||||||  |||||| ||| |||
---acgatgctgaaggttataatgacttaa-aataacaagttttaatgttgagaagtttctgctataatgacttacgtatgttgatttaaatctca-attttcagGAAAATATGTTGGAAATAGGCCAATCAAACTACGTAAGAGCAATTGGAGGGAGAGGACAGATTTTGAAGCCTTGGAAAGACAAAAG

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|208251032|gb|GE047355.1|GE047355
EST:     GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATG                         GAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGG
genomic: GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATGgttagtaagt ... ttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGG
EST: gi|208153822|gb|GD954791.1|GD954791
EST:     GTTAAAGAAATGAATG                         GAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTAGAAGG
genomic: GTTAAAGAAATGAATGgttagtaagt ... ttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGG
EST: gi|208290546|gb|GE087608.1|GE087608
EST:     GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATG                         GAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGG
genomic: GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATGgttagtaagt ... ttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGG
EST: gi|193432436|gb|FK396474.1|FK396474
EST:     GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATG                         GAAAGTATGTTGGAAATCGGCCGATAAAACTACG
genomic: GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATGgttagtaagt ... ttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACG
EST: gi|6725839|gb|AW310238.1|AW310238
EST:     GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATG                         GAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGG
genomic: GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATGgttagtaagt ... ttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGG
EST: gi|207740117|gb|GD714727.1|GD714727
EST:     GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATG                         GGAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGG
genomic: GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATGgttagtaagt ... ttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGG
EST: gi|193531570|gb|FK493168.1|FK493168
EST:     GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAA-TGAATG                         GAAAGTNTGTTGGAAATCGGCCGATAAAACTACG
genomic: GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATGgttagtaagt ... ttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACG
EST: gi|193573450|gb|FK530145.1|FK530145
EST:     GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATG                         GAAAGTATGTTGGAAATCGG
genomic: GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATGgttagtaagt ... ttggtttcagGAAAGTATGTTGGAAATCGG
EST: gi|6566353|gb|AW234022.1|AW234022
EST:     GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATG                         GAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGG
genomic: GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATGgttagtaagt ... ttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGG
EST: gi|193331635|gb|FK295447.1|FK295447
EST:     GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATG                         GAAAGTATGTTGGAAATCGGCCGATAAAAC
genomic: GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATGgttagtaagt ... ttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAAC
EST: gi|193427544|gb|FK393542.1|FK393542
EST:     GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATG                         GAAAGTATGTTGGAAATCGGCCGATAAAACTACG
genomic: GAGCTTTGCCAATCCTGCTGACCTTGCTGCTGCTGTTAAAGAAATGAATGgttagtaagt ... ttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattgtggccaatgcaatcaaatatgtatcctgactatgatgtcttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAG
                             tcctgac  putative branch site (score: 2)
                aatcaaatatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggcttatccaatttgtctctgaatcttgtcaatgtaaggagacaatattgtggccaatgcaatcaaatatgtatcctgactatgatgtcttggtttcagGAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - -ctctgaa
- - - - - - - - - - - - -cttgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - ccaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtc