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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtttgctattgcattaagaggagcaaagtacaactttcaactttattaaaacctagtttttatcttgtgattattccttgtgtttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAGACAAGCTTGT

Basic information

species Glycine max
transcript GLYMA05G34790.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 13
gtatgtgtttgctattgcattaagaggagcaaagta-caactttcaactttattaaaacctagtt--tttatcttg-tgattattccttgtgtttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAGACAAGCTTGT
  ||    |    ||    |  |    |   || ||   | |  ||      | |  |  |   |   | | |  | || |||| |||  | | | ||  |||||||||| || ||||||||||||||||| || ||||| ||| | || ||| ||||||| ||||| |  || || || || || |||| || | |     |
-cat-caatgaaaatcaagtggatcacatttaaataatgagtcacactgcagtcaggatatgactagctcaccaggatgcttatacctactatgt-tgtttagGTTCTGATCACATTCGTGAGAAAGATGGTATTTGGGCTGTTCTAGCATGGTTATCTATTCTTGCTTTCAAGAACAAGGACAACCTTGGAGGCGATAAGCT

upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 13
gtatgtgtttgctattgcattaagaggagcaaagtacaactttcaactttattaaaacctagttttta---tcttgtgattattccttgtgtt--tgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAG---ACAAGCTTGT
   || ||| |   |  ||| ||    | | |     || |       || ||   |  | || |  |   | ||| |||  ||   |||  |  | ||| |||| |||||||| ||||||||||||||||| |||||||| ||  | || ||||| |||||  |||| |  || ||||| || || |||| ||   | |||||   
--ttgagttagtggt--catgaatccaacccatagtaaagtcaaggacttgttggtatttggtatagacattattgagatgtttatatgtactactttggctagGGTCTGACCACATTCGTGAGAAAGATGGCATCTGGGCTGTGCTTGCATGGCTTTCTATTATTGCTTTCAAGAATAAGGACAACCTTGGAGGAGATAAGCT---

upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 13
gtatgtgtttgctattgcattaagaggagcaaa-gtacaactttcaactttattaaaacctagtttttatcttgtgattattccttgtgtttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAGACAAGCTTGT
                       |||   | |  |    |  ||||  | | ||||||||                | |         | || | || |||||| || ||||| |||||||||||||| |||||||||||| | || |||||||| ||||| ||  | || || || || |  ||||| |  ||      
---------------------gtgagcttctattgctagatcttcacatgttttaaaaccgtaacaaccctacacaactcacaaagaagcttttcgacagGTTCGGATCATATCCGTGAGAAAGATGGGATCTGGGCAGTTCTTGCTTGGCTATCAATACTGGCTCACAAGAACAAGGAAACCCTTGATGGGAATGCAAA

upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 14
gtatgtgtttgctattgcattaagaggagcaaagtacaactttcaactttattaaa-acctagtttttatcttgtgattattccttgtgtttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGA---AGACAAGCTTGT
        | | | |   |||  | | |  ||| |    || | || | |   | | || ||  |       | |  | ||   |||| | |  ||| |||||| ||||| |||||||||||||||||||||||||| ||||| || ||||| ||||| || || ||| ||||||| || || ||||    ||  |||||   
-------gtaggtttcatattttgtgtatgaaattt---ctgttaattatgacatacacatatgtaaagcaatattttgatctgttgtatctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGCTTTCTATTCTCGCTTATGAAAATAAGGAAAACCTTGGTGGAGCAAAGCT---

upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S4_12V6.3 (Physcomitrella patens), 3'ss of exon 14
-----------------------------------------------------------------------------------------gtatgtgtttgct-attgcattaagagga-gcaaagtacaactttcaactttattaaaacctagtttttatcttgtgattattccttgtgtt----tgtgg----atagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAGACAAGCTTGT
                                                                                         || ||  |  | | |   |||| | |    || |  ||     || |   |  || |||    ||||   |  |||  || ||  |||   |       ||      |||||||||||| ||| | ||||| |||||||| ||||| |||||||| ||||| ||||| |||||  | |  || ||  |      ||  |||||||||||
gtctacgctcattgcatccctcatcgtcaatgccttgcagtttgaaaaagttgtgttggactaatcttattaatggttattctttcatggtttgcttgggttcacgacatttataaactgcgatttatgtacttgagagtagtttaaaa--ggtttaagtggtgtttttgttttttgaactatggcacggtcttgcagGTTCTGACCACATTAGAGAGAAGGATGGAATTTGGGCCGTTTTGGCATGGCTCTCTATCCTTGCTCACAGGAACAAGCAGGCTGGTGGTGACAAGCTTGT

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|6567274|gb|AW234885.1|AW234885
EST:     AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG                         GTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
genomic: AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgttt ... ttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
EST: gi|12774378|gb|BG239305.1|BG239305
EST:     GTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG                         GTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
genomic: GTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgttt ... ttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
EST: gi|254347114|gb|GR856784.1|GR856784
EST:     AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG                         G-TCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
genomic: AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgttt ... ttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
EST: gi|17154046|gb|BM143979.1|BM143979
EST:     AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG                         GTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
genomic: AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgttt ... ttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
EST: gi|16349332|gb|BI974927.1|BI974927
EST:     AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG                         GTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
genomic: AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgttt ... ttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
EST: gi|27426004|gb|CA937524.1|CA937524
EST:     AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG                         GTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGTC
genomic: AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgttt ... ttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
EST: gi|208099059|gb|GD893926.1|GD893926
EST:     AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG                         GTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
genomic: AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgttt ... ttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
EST: gi|13312878|gb|BG406529.1|BG406529
EST:     AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG                         GTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
genomic: AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgttt ... ttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
EST: gi|21600532|gb|BQ610863.1|BQ610863
EST:     AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG                         GTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
genomic: AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgttt ... ttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
EST: gi|193518365|gb|FK476650.1|FK476650
EST:     TTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG                         GTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
genomic: TTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgttt ... ttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
EST: gi|7458620|gb|AW666070.1|AW666070
EST:     AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG                         GTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
genomic: AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgttt ... ttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactttattaaaacctagtttttatcttgtgattattccttgtgtttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAGACAAGCTTGT
               tagtttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtttgctattgcattaagaggagcaaagtacaactttcaactttattaaaacctagtttttatcttgtgattattccttgtgtttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAGACAAGCTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT