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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcctgcttcaaaaaattttctttgatttgcgttatatacaaatttaaattcttataacttctataatgtgtggctccctctttccttcattacagtttctttaaatttaaccaataaattttttttatgttgcttattataattcttttcttattatgtttttgcttttgcagATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAGAAATTTCCGGACATGATTATAAAG

Basic information

species Glycine max
transcript GLYMA10G04480.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 5
gtaagtttcctgcttcaaaaaattttctttgatttgcgttatatacaaatttaaattcttataacttctataatgtgtggctccctctttccttcat-tacagtttctttaaatttaaccaataaattttttttatgttgcttattataattcttttcttattatgtttttgcttttgcagATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAGAAATTTCCGGACATGATTATAAAG
                                                                       ||    |    |  |   |  || || | ||  |||    | || |    |||    || || |  |  |||  | ||     |  || |||   ||    | ||| ||| | || || || || || |||||||||||||| |||||||| ||||||||||| |  || || ||||| || |||
-----------------------------------------------------------------------aagaattaaaccattaggtagttaatatgcatgttcccctatttcag---ataggggttcttgactt--cttgctgtagac--taactgatt---ttcactcattttcagCTCATTATAGCGTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCAGAGAAGTACCCTGATATGATCATCAAG

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 5
gtaagtttcctgcttcaaaaaattttctttgatttgcgttatatacaaatttaaattcttataacttctataatgtgtggctccctctttccttcattacagtttctttaaatttaaccaataaattttttttatgttgcttattataattcttttcttattatgtttttgcttttgcagATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAGAAATTTCCGGACATGATTATAAAG
                                                                          ||     |  ||   | |       || | || ||    | ||    |   | | |||||||  | || || |||  ||  | |     || ||   | ||| ||| | || |||||||| || |||||||||||||| |||||||| ||||| ||||| | ||| || |||||||| |||
--------------------------------------------------------------------------gtcaaagtaacttaatgcacatcatcaatctcctttttctgaaatggttg-tatattttatgaagttttttttaaccctcatttc----tgattgcccattt-cagCTCATTATTGCTTGCAGCAAGGGAGGAACCAGTATTGAAGATCTTGCGGAGAAGTATCCTGATATGATTATTAAG

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtttcctgcttcaaaaaattttctttgatttgcgttatatacaaatttaaattcttataacttctataatgtgtggctccctctttccttcattacagtttctttaaatttaaccaataaattttttttatgttgcttattataattct----tttcttattatgtttttgcttttgcagATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAGAAATTTCCGGACATGATTATAAAG
                                                                                     || | ||   |||   || | ||   |||| | ||  |||||    ||       |   | ||| | |    | | |  | |  | ||    | | ||||| |||||||| ||||| ||||||||||||||||| |||||||||||||||||||| || ||||||||| | |||
------------------------------------------------------------------------------------gtcctgcccatatttgtgtgttttaccattttatcatgaaattacacttgaaaatatagatctaaatttaagatgtttactcacatattctgctctccagATCATAATTGCATGTAGAAAGGGAGGAACCAGCATCGAAGACCTTGCAGAGAAATTCCCTGACATGATTGTCAAG

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S9_103V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaagtttcctgcttcaaaaaattttctttgatttgcgttatatacaaatttaaattcttataacttctataatgtgtggctccctctttccttcattacagtttctttaaatttaaccaataaattttttttatgttgcttattataattcttttcttattatgttt-----ttgcttttgcagATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAGAAATTTCCGGACATGATTATAAAG
                                                                                     | |||  || ||    |||  ||  ||   || || |  ||   || ||  |    ||  ||  | || ||   | ||  | |     | |  || |||| | || ||||||||   |||||| ||||||||||| || |||||||| ||||||| ||||||   |||||| |||
-------------------------------------------------------------------------------------tgttttttttatctgtgttatttgtaagcaaagcacttgatcgattgtacttgttatacgatggtactgttaggactaaatctgaaggtggtgttggcagGTCATGATTGCTTGCGCTAAGGGTGGAACCAGCATAGAGGACCTTGCTGAGAAATATCCGGATCAGATTATCAAG

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|17518793|gb|BM187835.1|BM187835
EST:     TAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCA                         ATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAG
genomic: TAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCAgtaagtttcc ... gcttttgcagATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAG
EST: gi|61241640|gb|DN591031.1|DN591031
EST:     TAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCA                         ATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAG
genomic: TAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCAgtaagtttcc ... gcttttgcagATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAG
EST: gi|15000418|gb|BI321232.1|BI321232
EST:     TAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCA                         ATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAG
genomic: TAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCAgtaagtttcc ... gcttttgcagATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAG
EST: gi|192308759|gb|FG999784.1|FG999784
EST:     TAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCA                         ATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCA
genomic: TAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCAgtaagtttcc ... gcttttgcagATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCA
EST: gi|151397308|gb|EV267181.1|EV267181
EST:     TAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCA                         ATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAG
genomic: TAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCAgtaagtttcc ... gcttttgcagATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAG
EST: gi|151409274|gb|EV279082.1|EV279082
EST:     TAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTGCA                         ATTATAATTGCTTGTAGTAAGGGAGGA
genomic: TAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCAgtaagtttcc ... gcttttgcagATTATAATTGCTTGTAGTAAGGGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttatgttgcttattataattcttttcttattatgtttttgcttttgcagATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAGAAATTTCCGGACATGATTATAAAG
                        ttcttttcttattatg  CT-rich tract
               ttattataattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttcctgcttcaaaaaattttctttgatttgcgttatatacaaatttaaattcttataacttctataatgtgtggctccctctttccttcattacagtttctttaaatttaaccaataaattttttttatgttgcttattataattcttttcttattatgtttttgcttttgcagATTATAATTGCTTGTAGTAAGGGAGGAACCAGCATTGAAGACCTTGCAGAGAAATTTCCGGACATGATTATAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA