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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ttttacccctattcttctatcacttacatttctaagttctaattgtgcacaagaatcttaagagtctctttttctctttttgaaaactcacatgaatagtttcgacattaaattttggatttcttagaCCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCCT

Basic information

species Glycine max
transcript GLYMA18G08230.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 7
ttttacccctattcttctatcacttacatttctaagttctaattgtgcacaagaatcttaagagtctctttttctctttttgaaaactcacatgaatagtttcgacattaaattttggatttcttagaCCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCCT
                       | |||| ||     |    ||| ||| |||| | |    ||| | | ||  |  |||| ||   | || |  |  | |   | | ||  ||||    ||  ||||| || ||||| ||||| |||||||||||||| | |||||| || ||||||||| | || || ||| | || ||||| ||  |  ||||||||||||| | 
----------------------atgacatatcctcaataggcttg-gcataaga-tatggtcagtttatcttgtttctttttaattgtaacttccaatgct---aaactattttttcttatttgtagACATTTGAGGAGGCAGACACAAAGCATGATGGAAGAATTGATAAAGAAGAGTGGCGCAATCTGGTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTC-

upper sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 7
ttttacccctattcttctatcacttacatttctaagttcta-attgtgcacaagaatcttaagagtctctttttctctttttgaaaactcacatgaatagtttcgacattaaattttggatttcttagaCCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCCT
                         ||||   |  |||    |||    | ||  |  ||   |  |||||  |  ||  |   ||| || |  |  || ||| |   |    || ||   ||   |||| || ||||| ||||| |||||||||||||| | ||||||||||||||||||| | || || ||  | || ||||| ||  |  ||||||||||||| | 
------------------------gacatcagtgggtttggcattagaaataatcagattgtcatcctcttgcttgctgatatcaaattccctcgc-taattttgttttc---ttctgtcattacaagACATTTGAGGAGGCAGACACAAAGCATGATGGAAGAATTGACAAGGAAGAGTGGCGCAATCTAGTCATTCGGCATCCTTCTTTGCTGAAGAACATGACTC-

upper sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 6
ttttacccctattcttctatcacttacatttctaagttctaattgtgcacaagaatcttaag--agtctctttttctctttttgaaaactcacatgaatagtttcgacattaaattttggatttcttagaCCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCCT
                 ||| ||||| ||   ||   || ||    |   ||   |   |||   |||    | | |  | ||  || || |  | | |  ||||         ||||   | |   |||| || ||||| ||||| |||||||||||||| ||||||||||| ||||| ||| | ||  | ||  || | ||||| ||  | |||||||||||||| | 
--------------gcttattacttaaataaata--ctccaaacaagtgaaaacgtgacaagttggtcagcctatgtgctatttgaatcttat-taagttttttc---------tttt---tctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAATGGCGCAATTTAGTAGTGAGGCATCCCTCTTTATTGAAGAACATGACAC-

upper sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 8
ttttacccctattcttctatcacttacatttctaagttctaattgtgcacaagaatcttaagagtctctttttctctttttgaaaactcacatgaatagtttcgacattaaattttggatttcttagaCCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCCT
                                                  |||   ||||    | | |  |  ||    |  |   |  | |  | |||     |    | ||||| || | | |||| || ||||||||||| ||||| || ||||| || || || |||||||||||||||| ||||||| |  | |||||    ||| ||||||||||||| | 
------------------------------------------------gtaagttacttactt-tttttcctcttcaccctatattttttctttgaaagtaatttc-ccgagttttgaatgtttcagACGTTTGAGGAAGCAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTC-

upper sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 6
ttttacccctattcttctatcacttacatttctaagttctaattgtgcacaagaatcttaagagtctctttttctctttttgaaaactcacatgaatagtttcgacattaaattttggatt-tcttagaCCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCCT
                        | | |   ||||    || | ||    | | ||      |  | | | | | ||      | |||  || |    |||  |  ||      || ||| |   ||||||| |||||||| || ||||| |||||||| || |||||||| ||||||||||||| ||||||| | || || || || ||||||||||| ||||| | 
-----------------------ctccttggttaagcagcaagt-tgagggaaactcaatttggattttgtatttgttgcatccatctcttataacctttttttattttgg----tgcattgttccagACCTTTGAGGAAGCTGACACAAAACATGATGGAAAGATTGACAAAGAAGAGTGGAGAAGCCTTGTTCTACGACACCCATCCCTTTTGAAGAATATGACTC-

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|151397479|gb|EV267352.1|EV267352
EST:     ATCTGGCATGAACCTATCAGATGACGTTATAGAAAGTATAATTGACAAGA                         CCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGT
genomic: ATCTGGCATGAACCTATCAGATGACGTTATAGAAAGTATAATTGACAAGGttttacccct ... atttcttagaCCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGT
EST: gi|8284959|gb|BE022518.1|BE022518
EST:     ATCTGGCATGAACCTATCAGATGACGTTATAGAAAGTATAATTGACAAGA                         CCTTCGAGGAAGCAGATACGAAGCATGATGGCAAAATTGACAAAGAAGAGT
genomic: ATCTGGCATGAACCTATCAGATGACGTTATAGAAAGTATAATTGACAAGGttttacccct ... atttcttagaCCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGT
EST: gi|13791269|gb|BG653860.1|BG653860
EST:     ATCTGGCATGAACCTATCAGATGACGTTATAGAAAGTATAATTGACAAGA                         CCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGT
genomic: ATCTGGCATGAACCTATCAGATGACGTTATAGAAAGTATAATTGACAAGGttttacccct ... atttcttagaCCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGT
EST: gi|192320225|gb|FK014239.1|FK014239
EST:     ATCTGGCATGAACCTATCAGATGACGTTATAGAAAGTATAATTGACA-GA                         CCTTCGAGGA-GCAGATACAAAGCATGATGGCAAA
genomic: ATCTGGCATGAACCTATCAGATGACGTTATAGAAAGTATAATTGACAAGGttttacccct ... atttcttagaCCTTCGAGGAAGCAGATACAAAGCATGATGGCAAA
EST: gi|254324275|gb|GR840592.1|GR840592
EST:     ATCTGGCATGAACCTATCAGATGACGTTATAGAAAGTATAATTGACA-GA                         CCTTCGAGGA-GCAGATACAAAGCAT
genomic: ATCTGGCATGAACCTATCAGATGACGTTATAGAAAGTATAATTGACAAGGttttacccct ... atttcttagaCCTTCGAGGAAGCAGATACAAAGCAT
EST: gi|308098080|gb|HO761251.1|HO761251
EST:     ATCTGGCATGAACCTATCAGATGACGTTATAGAAAGTATAATTGACAAGA                         CCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGT
genomic: ATCTGGCATGAACCTATCAGATGACGTTATAGAAAGTATAATTGACAAGGttttacccct ... atttcttagaCCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctttttgaaaactcacatgaatagtttcgacattaaattttggatttcttagaCCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCCT
           aactcac  putative branch site (score: 2)
                                              tttctt  putative PPT
                                 attaaattttggattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttacccctattcttctatcacttacatttctaagttctaattgtgcacaagaatcttaagagtctctttttctctttttgaaaactcacatgaatagtttcgacattaaattttggatttcttagaCCTTCGAGGAAGCAGATACAAAGCATGATGGCAAAATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC