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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacttcctttttttctcattggattatttaatttttccttttccttttggtatcacaaggtatgttgattactttttctctgttaactactcttctcagATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAG

Basic information

species Glycine max
transcript GLYMA16G05140.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G05140.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g16940.1 (Oryza sativa), 3'ss of exon 2
gtaagcacttcctttttttctcattggattatttaatttttccttttccttttggtatcacaaggtatgttgattactttttctctgttaactactcttctcagATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAG
||||||          || ||  |     |  ||| |||| | |       |    |   | |  |  |||| ||  ||||| |   | ||  |        ||||||||||||| || || || ||||||||||| ||||| ||||||||||| || || || ||||| ||||| | |||     || |        ||
gtaagc---------cttgcttgtcacgatgcttacttttgcttcagtggatactaactgctaattgggttgtttgtttttttttcctgaaacat-------agATAATATACCTTGGGAAGCCAGATGGGCCTACTTGCCATACAGGGGCAGAGACTTGTTACTATACTTCAGTCTATGATGCTCTACAAGGTTCGAAG

upper sequence: GLYMA16G05140.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G082214_T01 (Zea mays), 3'ss of exon 2
gtaagcacttcctttttttctcattggattatttaatttttccttttccttttggtatcacaaggtatgttgattactttttctctgttaactactcttctcagATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAG
|||||||  |  | | ||      || || | |  | |||  |||    || ||     || |  |     ||    || || | |||  |        || ||||||||||||| ||||| || ||||| ||||||||||| ||||| |||||||| || |||||||| ||||||| |||     || |      | ||
gtaagcatgttatgtgttg-----tgaataaat--actttcacttcgatttctgagggtactaactgcacagagcttttgttttttgtgcaa-------cttagATAATATACCTTGGAAAGCCAGATGGACCTACCTGCCATACAGGAGCAGAAACGTGTTATTATACTTCAGTTTATGATGCTCTACAAAGTTCAAAG

upper sequence: GLYMA16G05140.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0068g00910.t01 (Vitis vinifera), 3'ss of exon 2
gtaagcacttcctttttttctcattggattatttaatttttccttttccttttggt--atcacaaggtatgttgattacttttt--ctctgttaactact-cttctcagATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAG
                         | ||  |||  ||  |||||||   || | |  || |    | | ||   ||    ||    |   ||    |||  |||||||||||||||||| || || ||||| |||||||| |||||||| ||  | ||||| ||||||||| ||||||| ||||| ||||||||  | |   ||
-------------------------gtatgttttttttactcctttttagttggatgcataaatgagcaggtcctttgtcattagatttgattctgaactatttctcagATAATATACCTTGGGAAGCCTGACGGGCCTACTTGCCACACTGGATCTGAAACTTGCTATTATTCATCAGTATTTGATTTGTTAAAAAATCCTCAG

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|151409476|gb|EV279284.1|EV279284
EST:     ATAATTTTATCAATGTTCACGATGTCTTTATTGATTGTGATCGTGATTCT                         ATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAA
genomic: ATAATTTTATCAATGTTCACGATGTCTTTATTGATTGTGATCGTGATTCTgtaagcactt ... ctcttctcagATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAA
EST: gi|6747878|gb|AW318334.1|AW318334
EST:     ATAATNTTATCAATGTTCACGATGTCTNTATTGATTGTGATCGTGATTCT                         ATAATATACCTGNGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAA
genomic: ATAATTTTATCAATGTTCACGATGTCTTTATTGATTGTGATCGTGATTCTgtaagcactt ... ctcttctcagATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAA
EST: gi|192295469|gb|FG987083.1|FG987083
EST:     ATAATTTTATCAATGTTCACGATGTCTTTATTGATTGTGATCGTGATTCT                         ATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAA
genomic: ATAATTTTATCAATGTTCACGATGTCTTTATTGATTGTGATCGTGATTCTgtaagcactt ... ctcttctcagATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAA
EST: gi|26058540|gb|CA801454.1|CA801454
EST:     ATAATTTTATCAATGTTCACGATGTCTTTATTGATTGTGATCGTGATTCT                         ATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAA
genomic: ATAATTTTATCAATGTTCACGATGTCTTTATTGATTGTGATCGTGATTCTgtaagcactt ... ctcttctcagATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAA
EST: gi|19934822|gb|BQ079852.1|BQ079852
EST:     ATAATTTTATCAATGTTCACGATGTCTTTATTGATTGTGATCGTGATTCT                         ATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAA
genomic: ATAATTTTATCAATGTTCACGATGTCTTTATTGATTGTGATCGTGATTCTgtaagcactt ... ctcttctcagATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAA
EST: gi|23056166|gb|BU577706.1|BU577706
EST:     ATAATTTTATCAATGTTCACGATGTCTTTATTGATTGTGATCGTGATTCT                         ATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAA
genomic: ATAATTTTATCAATGTTCACGATGTCTTTATTGATTGTGATCGTGATTCTgtaagcactt ... ctcttctcagATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggtatcacaaggtatgttgattactttttctctgttaactactcttctcagATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAG
                                    tgttaac  putative branch site (score: 2)
                                          ctactcttctc  CT-rich tract
                       attacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcacttcctttttttctcattggattatttaatttttccttttccttttggtatcacaaggtatgttgattactttttctctgttaactactcttctcagATAATATACCTGGGAAAACCTGATGGGCCTACCTGCCACACAGGGGCAGAAACATGCTATTATACATCAGTTTTTGACTTGTTAAAGCAGCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA