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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacagtggcatattttgatttatcttctagttaaactaggttggtatcatatttaagaaatgcatgtgcctaatttagaaaatttgccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAAATTATGACGGTGGCCGTGATTTGGATGATTTTGTAGCA

Basic information

species Glycine max
transcript GLYMA19G41690.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G41690.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 7
-----gtgagtacagtggca-tattttgatttatcttctagttaaactaggttggtatcatatttaagaaatgcatgtgcctaatttagaaaatttgccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAAATTATGACGGTGGCCGTGATTTGGATGATTTTGTAGCA
      || | |   |  ||  | ||| |  |    ||| |||  | ||  ||| | ||||  |   | | | |||  |  |    | |     |  |   |  |||||||| |||  ||||||||||||| ||||||| ||||||||| | ||||||||||||||| |||| || || ||| | || |||||||| |||||    
atgttatgggcatgcttccagcactttaaactcatgtcttgttcta-tattttgatttcatgat---gcactacataagttttgacttgctttatgact--tttagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTACGATGGCGGCAGGGAGTTGGATGACTTTGTCAAG

upper sequence: GLYMA19G41690.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G128171_T04 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------------gtgagtacagtggcatattttgatttatcttctagt--taa--actag-----gttggtatca-------------tatttaagaaatgca-tgtgcctaatttagaaaatttgcca----ata-cagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAAATTATGACGGTGGCCGTGATTTGGATGATTTTGTAGCA
                                                                    |  || || |  ||||  | |  |||  |||  | |  ||   |||||     ||| | | ||             |||||  ||  ||   | | |  ||| ||    | ||  ||    | | ||| ||||| |||||||| | ||||||  ||||||||||||||||| | ||||||||||||||| ||||||| || |   | || |||| ||| |||||    
gtatgttctgtgtcttacattcacatatgctttatctgcatctgtttccctatttgtgttacctagcagctagcactggagcatgatcttgtttccctttgaatactagtcactagtatttgtttgcaacaaataacaccttattatttctgacttgttctatacgcaatatactgtacttatcacactacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG

upper sequence: GLYMA19G41690.1 (Glycine max), 3'ss of exon 7
lower sequence: AC217311.3_FGT007 (Zea mays), 3'ss of exon 1
gtgagtacagtggcatattttgatttatcttctagttaaactaggttggtatcatatttaagaaatgcatgtgcctaatttagaa-aatttgccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAAATTATGACGGTGGCCGTGATTTGGATGATTTTGTAGCA
                                                ||||    | |   |  | ||   || |  || | || ||| | ||  | |||||||||||||  ||| |  |||||| ||||||| ||||| ||| | |||||||| |||||| ||||||| |||||||| || |||||||| |||||    
------------------------------------------------gtatgcattcttccatgttcaca-gcatctttaataataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA19G41690.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G159369_T01 (Zea mays), 3'ss of exon 7
gtga-gtacagt--ggcatattttgatttatcttctagttaaactaggttggtatcatatttaagaaatgcatgtgcctaatttagaaaatttgccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAAATTATGACGGTGGCCGTGATTTGGATGATTTTGTAGCA
 |||   || ||  || |||     |  |||   | | ||| | ||  |  || |    |||     |||       |   |||| | ||| | ||  | |||||||||||||  ||| |  |||||| ||||||| ||||| ||| | |||||||| |||||| ||||||| |||||||| || |||||||| |||||    
-tgacagactgttagggataacacaacctatga-caatttataataactacgtttgtcctttcttccatgttcacagcatcttta-ataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA19G41690.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G110742_T02 (Zea mays), 3'ss of exon 7
gtgagtacagtggcatattttgatttatcttctagttaaactaggttggtatcatatttaagaaatgcatgtgcctaatttagaaaatttgccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAAATTATGACGGTGGCCGTGATTTGGATGATTTTGTAGCA
                                            ||  | ||  | |  | |      |  |   ||||    | ||| | ||  | |||||||||||||  ||| |  |||||| ||||||| ||||| ||| | |||||||| |||||| ||||||| |||||||| || |||||||| |||||    
--------------------------------------------gtatgcattct-tccatgttcacaacatctttaat---aataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA19G41690.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G404011_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------------------------------------gtgagtacagtggcatattttgatttatcttctagttaaactaggttggtatcatatttaagaaatgcatgtgcctaa----tttagaa--aatttgccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAAATTATGACGGTGGCCGTGATTTGGATGATTTTGTAGCA
                                                                                       | || |    ||  | | |||  |      || |   ||   |   |    || | |   ||| ||| |||| |  ||    ||||  |  ||| | ||  | |||||||||||||  ||| |  |||||| ||||||| ||||| ||| | |||||||  |||||| ||||||| |||||||| || |||||||| |||||    
gtatgcattctgacttgtctatttcagtggttgttatgcacattagctttcagcctttagtttaacaccattggattttcttatatggcgattgtgatgaaaaaatttcctcaggaatc-acagaagtgattctctcgtcgtttgacagatatggatgttcacaacatctttaataataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGTCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA19G41690.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G008647_T02 (Zea mays), 3'ss of exon 4
-----gtgagtacagtggcatattttgatttatcttctagttaaactaggttggtatcatatttaagaaatgca-tgtgcctaatttagaaaatttgccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAAATTATGACGGTGGCCGTGATTTGGATGATTTTGTAGCA
     |    |  | |   |||  |      || || || |  ||||| ||| ||    | ||  |      ||   |   ||||    | ||| | ||  | |||||||||||||  | | |  |||||| ||||||| ||||| ||| | |||||||| |||||| ||||||| |||||||| || |||||||| |||||    
caaaagcatctttaataatatacctatgacaat-ttataat--aactatgtttgtcctttcttccatgttcacagcatctttaat---aataatatacctctgcagATATGGTGTTTCTAGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA19G41690.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G170845_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------------------------gtgagtacagtggcatattttgatttatcttctagttaaactaggttggtatcatatttaagaaatgcatgtgcctaa----tttagaa--aatttgccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAAATTATGACGGTGGCCGTGATTTGGATGATTTTGTAGCA
                                                                                         || |    ||  | | |||   | ||     |   ||   |   |    || | |   ||| ||| |||| |  |     ||||  |  ||| | ||  | |||||||||||||  ||| |  |||||| ||||||| |  || ||| | |||||||| |||||| ||||||| |||||||| || |||||||| |||||    
gtatgcattctgacttgtctatttcagtggttgttatgcacattagctttcagcctttagtttaacaccactggattttcttatattacgattgtgatgaaaaaatttc-ctcatgaatcacagaagtgattctctcgtcgtttgacagatatggatgttcacagcatctttaataataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTATCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

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|151396704|gb|EV266577.1|EV266577
EST:     GTAGTTATAGCCAATGTTGATGCCGACAAGTATAAAGATTTGGCCGAGAA                         ATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
genomic: GTAGTTATAGCCAATGTTGATGCCGACAAGTATAAAGATTTGGCTGAGAAgtgagtacag ... gccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
EST: gi|7146459|gb|AW508381.1|AW508381
EST:     GTAGTTATAGCCAATGTTGATGCCGACAAGTATAAAGATTTGGCTGAGAA                         ATATGGTGTTAGTGGCTATCCTACACTGAAAGTTTT-CCCAAAGAGCAACA
genomic: GTAGTTATAGCCAATGTTGATGCCGACAAGTATAAAGATTTGGCTGAGAAgtgagtacag ... gccaatacagATATGGTGTTAGTGGCTATCCTACACTGAA-GTTTTTCCCAAAGAGCAACA
EST: gi|208225238|gb|GE022255.1|GE022255
EST:     GTAGTTATAGCCAATGTTGATGCCGACAAGTATAAAGATTTGGCTGAGAA                         ATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
genomic: GTAGTTATAGCCAATGTTGATGCCGACAAGTATAAAGATTTGGCTGAGAAgtgagtacag ... gccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
EST: gi|7327245|gb|AW620967.1|AW620967
EST:     GTAGTTATAGCCAATGTTGATGCCGACAAGTATAAAGATTTGGCTGAGAA                         ATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
genomic: GTAGTTATAGCCAATGTTGATGCCGACAAGTATAAAGATTTGGCTGAGAAgtgagtacag ... gccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
EST: gi|21600775|gb|BQ611106.1|BQ611106
EST:     GTAGTTATAGCCAATGTTGATGCCGACAAGTATAAAGATTTGGCTGAGAA                         ATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
genomic: GTAGTTATAGCCAATGTTGATGCCGACAAGTATAAAGATTTGGCTGAGAAgtgagtacag ... gccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
EST: gi|58024257|gb|CX710998.1|CX710998
EST:     GTAGTTATAGCCAATGTTGATGCCGACAAGTATAAATATTTGGCTGAGAA                         ATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
genomic: GTAGTTATAGCCAATGTTGATGCCGACAAGTATAAAGATTTGGCTGAGAAgtgagtacag ... gccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
EST: gi|209720793|gb|BW657767.1|BW657767
EST:     GTAGTTATAGCCAATGTTGATGCCGACAAGTATAAAGATTTGGCTGAGAA                         ATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA
genomic: GTAGTTATAGCCAATGTTGATGCCGACAAGTATAAAGATTTGGCTGAGAAgtgagtacag ... gccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtatcatatttaagaaatgcatgtgcctaatttagaaaatttgccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAAATTATGACGGTGGCCGTGATTTGGATGATTTTGTAGCA
                           gcctaat  putative branch site (score: 3)
                              taatttagaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtacagtggcatattttgatttatcttctagttaaactaggttggtatcatatttaagaaatgcatgtgcctaatttagaaaatttgccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAAATTATGACGGTGGCCGTGATTTGGATGATTTTGTAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG