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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagaccctttaagtttttgtgtaatgtaatcatagtcttaatagttactacagtattgaactctctgttgtaaactatttctgctaagcacattctacttctgttgcagGGTTGCTATGTCTGCATTGTCACTGGATACTGTGAAGGTGGAGACAT

Basic information

species Glycine max
transcript GLYMA11G18340.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 3
gtgagagaccctttaagtttttgtgtaatgtaatcatagtcttaatagttactacagtattgaactctctgttgtaaactatttctgctaagcacattctacttctgttgcagGGTTGCTATGTCTGCATTGTCACTGGATACTGTGAAGGTGGAGACAT
                                 |  | |  |    | |||||| |    |    | |||| | || |||  ||  | | | ||      | |     |||||||||||||||||||||||||||| || || |||||||||||||| ||
-------------------------------gtttgtggattaggaacttactatatc--tagcttatctggtttatacttatttagttga-catgggtcagt---aatgcagGGTTGCTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGATAT

upper sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G137118_T02 (Zea mays), 3'ss of exon 4
gtgagagaccctttaagtttttgtgtaatgtaatcatagtcttaatagttactacagtattgaactctctgttgtaaactatttctgctaagcacattctacttctgttgcagGGTTGCTATGTCTGCATTGTCACTGGATACTGTGAAGGTGGAGACAT
                             ||  |  ||||      | ||  |      |||     |||||| | ||||  ||  | | |  |  |   | || ||   |||||||| ||||||||||||||||| || || |||||||||||||||||
-----------------------------gtt-ttgtagttcaggaacttgttcttaccttgtttcttctgtt-tgaacttatttagttgacaaggtg--agttatg---cagGGTTGTTATGTCTGCATTGTCACGGGCTATTGTGAAGGTGGAGACAT

upper sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G074262_T01 (Zea mays), 3'ss of exon 4
gtgagagaccctttaagtttttgtgtaatgtaatcatagtcttaatagttactacagtattgaactctctgttgtaaactatttctgctaagcacattctacttctgttgcagGGTTGCTATGTCTGCATTGTCACTGGATACTGTGAAGGTGGAGACAT
                                 |  |  |      |  | || | |||||   || |   |||    |    |||| ||     |  |      | |   |||| |||||||| |||||||| || ||||||||||||||||| || ||
-------------------------------gttggttcttcatgaacatgcttctgtatttgccttttatttggttccgtcctctgttacctcaacgcatgagttttgatagGGCTGCTATGTTTGCATTGTGACGGGATACTGTGAAGGTGGCGATAT

upper sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagagaccctttaagtttttgtgtaatgtaatcatagtcttaatagttactacagtattgaactctctgttgtaaactatttctgctaagcacattctacttctgttgcagGGTTGCTATGTCTGCATTGTCACTGGATACTGTGAAGGTGGAGACAT
                        ||||  |   |||    || ||   |  ||  |  || || |   | | || ||    || || || |  |    |        |||||||||||||||| || ||||||||||||||||||||||| ||||||||
------------------------gtaagttttacatcactttgat---ttttatggatttaaagtagatttggttaaaggattttgataggagctagatttgaaaaatgcagGGTTGCTATGTTTGTATTGTCACTGGATACTGTGAAGGAGGAGACAT

upper sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 3
gtgagagaccctttaagtttttgtgtaatgtaatcatagtcttaatagttactacagtattgaactctctgttgtaaactatttctgctaagcacattctacttctgttgcagGGTTGCTATGTCTGCATTGTCACTGGATACTGTGAAGGTGGAGACAT
               || |  ||   | | || |     | || |    |  |   |   | ||  |    |||||       |      ||  | ||    ||    |||||||||||||||| ||||||||||||||||| |||||||| ||||||||
-------------gtaggtcctggaaattctagtt----ttttgacgaatttttttgctgtaaatgcgaccttgta------ctgaatcgagagc-tttgggttggaatgcagGGTTGCTATGTTTGCATTGTCACTGGATATTGTGAAGGAGGAGACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgaactctctgttgtaaactatttctgctaagcacattctacttctgttgcagGGTTGCTATGTCTGCATTGTCACTGGATACTGTGAAGGTGGAGACAT
                                      ttctacttct  CT-rich tract
                taaactattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagagaccctttaagtttttgtgtaatgtaatcatagtcttaatagttactacagtattgaactctctgttgtaaactatttctgctaagcacattctacttctgttgcagGGTTGCTATGTCTGCATTGTCACTGGATACTGTGAAGGTGGAGACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA