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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGGCTGCCCGCCAAGAATCTCATGGCGGAGAGGCGCCGCCGGAAGAAGCTCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAGgtatgactaacaaaaaccacaaaatttggttttggaaataattatttattaactgttggtcattactggttttgtttcaatgtttgttctcttgttgttc...

Basic information

species Glycine max
transcript GLYMA19G27480.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G27480.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os11g32100.1 (Oryza sativa), 5'ss of exon 1
GGGGCTGCCCGCCAAGAATCTCATGGCGGAGAGGCGCCGCCGGAAGAAGCTCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAGgtatgactaacaaaaaccacaaaatttggttttggaaataattatttattaactgttggtcattactggttttgtttcaatgtttgttctcttgttgttc-
|||| |||| |||||||| |||||||||||| | |||||||||||||||||||| ||  |  | ||||||||| | || || || |||||||| ||||||||  |  |  |     |  |         || |    | |  | |  |  |  | ||  |  |  |   ||||     |    |  || |  |    ||  
GGGGATGCCGGCCAAGAACCTCATGGCGGAGCGCCGCCGCCGGAAGAAGCTCAACGACCGCCTCTACATGCTCCGCTCCGTCGTGCCCAAGATCAGCAAGgtcaggattccttctcctgctct-cccaattctcatgaaatctctcaaaaagttcttaattctggcgaattttagggaatgcgtaattttggtcgaatttt

upper sequence: GLYMA19G27480.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os01g70310.1 (Oryza sativa), 5'ss of exon 2
GGGGCTGCCCGCCAAGAATCTCATGGCGGAGAGGCGCCGCCGGAAGAAGCTCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAGgt-atgactaacaaaaaccacaaaatttggttttgga--aataattatttattaactgttggtcattactggttttgtttcaatgtttgttctcttgttgttc
|||| |||| |||||||| |||||||||||| |||| ||| ||||||||||||| ||  |  | ||||||||  | || || || |||||||| |||||||| || | | ||   |     |   |||   | |  |    |||||||||| | |   |  |    | | | || |  |  | ||| | || |    |   | 
GGGGATGCCGGCCAAGAACCTCATGGCGGAGCGGCGGCGCAGGAAGAAGCTCAACGACCGCCTCTACATGCTGCGCTCCGTGGTGCCCAAGATCAGCAAGgtgattaatgacctcatttctattttttcactgttcattgctaattatttaatta--atcagcagctccagtttctactagactgtatcttattaattaaat-

upper sequence: GLYMA19G27480.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G033356_T01 (Zea mays), 5'ss of exon 1
GGGGCTGCCCGCCAAGAATCTCATGGCGGAGAGGCGCCGCCGGAAGAAGCTCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAGgtatgactaacaaaaaccacaaaatttggttttggaaataattatttattaactgttggtcattactggttttgtttcaatgtttgttctcttgttgttc------
|||| |||| |||||||| |||||||| ||| | || |||||||||||||| |||||  || | ||||||||| |||| || || |||||||| ||||||||| || |   |    ||     || |   | ||  ||| | |   ||  || ||| | || | | |    |   |||   |  | |||  | |   ||       
GGGGTTGCCGGCCAAGAACCTCATGGCAGAGCGCCGTCGCCGGAAGAAGCTTAATGACCGGCTCTACATGCTCCGGTCCGTCGTGCCCAAGATCAGCAAGgtaagaattgta----cctttgcatcta--tgtgttaatcagttactacgaattgtagctcgtaatttagatgaattctccgcgttttcggtagcaattagcaact

upper sequence: GLYMA19G27480.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G172297_T01 (Zea mays), 5'ss of exon 1
GGGGCTGCCCGCCAAGAATCTCATGGCGGAGAGGCGCCGCCGGAAGAAGCTCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAGgtatgactaacaaaaaccacaaaatttggtt-ttggaaataattatttattaactgttggtcattactggttttgtttcaatgtttgtt-ctcttgttgttc-
| || |||| |||||||| |||||||||||| | || |||||||||||||| |||||  || | ||||||||| | || || || |||||||| ||||||||  || |   |           ||||| |  | ||  |  || | || | | ||  |  |  |||   |  || |   ||| || ||  |  ||    |   
GAGGTTGCCGGCCAAGAACCTCATGGCGGAGCGCCGTCGCCGGAAGAAGCTTAATGACCGGCTCTACATGCTCCGATCCGTCGTGCCCAAGATCAGCAAGgtgagaattgtaccctttcatccatttgttaatcggctactatgaattgt-agctcgtaat--ttagatgaattctccgaattttggtagcaattagcatctg

upper sequence: GLYMA19G27480.1 (Glycine max), 5'ss of exon 1
lower sequence: AT3G26744.2 (Arabidopsis thaliana), 5'ss of exon 2
GGGGCTGCCCGCCAAGAATCTCATGGCGGAGAGGCGCCGCCGGAAGAAGCTCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAGgtatg-actaacaaaaaccacaaaatttggttttggaaataattatttatta--actgttggtcattactg-gttttgtttcaatgtttgttctcttgttgttc------------------------------------------------------------------------------
 ||  |||| || |||||||| ||||| |||||| |  |  |||||||||| ||||||||| | || ||||| || || |||||||||||||| ||||| |||   ||| ||     |      || |  ||  |    |  ||| || ||     | | |   |||  || ||| |   |   |      | | |||||||                                                                                
AGGTATGCCTGCTAAGAATCTGATGGCTGAGAGGAGAAGGAGGAAGAAGCTTAATGATAGGCTTTATATGCTTAGATCAGTTGTCCCCAAGATCAGCAAAgtaaacacttactttgtctcttttatctccttaagagcttgtttacttgttgctgttatagagaattgttgtgttgtagctttgtagggcctttgttgttgtcaaactttgcatgtagttgctttactcttttgaggaagaggctcgtgatagtgttttatggattttcgatgaatttgcag

upper sequence: GLYMA19G27480.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv01s0244g00130.t01 (Vitis vinifera), 5'ss of exon 1
GGGGCTGCCCGCCAAGAATCTCATGGCGGAGAGGCGCCGCCGGAAGAAGCTCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAGgtatgactaac---aaaaaccacaaaatttggttt---tggaaataattatttattaactgttggtcattactggttttgtttcaatgtttgttctcttgttgttc
||||||||| || |||||| | ||||| |||||||||||  | |||||||| || |||||| | |||||||| ||||||||||| || ||||| ||||||||  || |         ||   ||   |  |||||   ||||  |     |   ||| |||    |  || ||  | || ||| ||| ||   |  | | |||   
GGGGCTGCCGGCGAAGAATTTGATGGCTGAGAGGCGCCGGAGAAAGAAGCTGAACGATAGGCTCTACATGCTGAGGTCTGTTGTTCCAAAGATCAGCAAGgtgagaattttctggtgaatttcagtgtggggtttgcttggatgtgggcctcgtttatctgaaaat--tttcttttcttttttaaattttctctagcct-ttg---

upper sequence: GLYMA19G27480.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ28242 (Selaginella moellendorffii), 5'ss of exon 1
GGGGCTGCCCGCCAAGAATCTCATGGCGGAGAGGCGCCGCCGGAAGAAGCTCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAGgtatg-actaacaaa--aaccacaaaatttggttttgga--aataattatttattaactgttggtcattactggttttgtttcaatgt---ttgttctcttgttgttc------------
||| || || ||||||||||||||||||||| |||| || ||||||||||| |||||| | |||||||||||  | || || |||||||| ||||  |||||  | |||  ||||  |  |    || ||||  ||           |  |  ||   ||    |   |  |  | |  | ||  | |   |   ||||   ||| |             
GGGCCTTCCGGCCAAGAATCTCATGGCGGAGCGGCGACGGCGGAAGAAGCTTAATGATCGCTTGTACATGCTTCGCTCGGTGGTCCCCAAAATTACAAAGgtgagtactttcaaaccactcgggcaacttggcattcactcgcccgctcctctttccatgcctttacctctttttctcctctcgctctcactcactctcaacttggtttgattttgtcag

upper sequence: GLYMA19G27480.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ29742 (Selaginella moellendorffii), 5'ss of exon 1
GGGGCTGCCCGCCAAGAATCTCATGGCGGAGAGGCGCCGCCGGAAGAAGCTCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAGgtatg-actaacaaa--aaccacaaaatttggttttggaaataattatttattaactgttggtcattactggttttgtttcaat-gtttgttctcttgttgttc------------------
||| || || ||||||||||||||||||||| |||| || ||||||||||| |||||| | |||||||||||  | || || |||||||| ||||  |||||  | |||  ||||  |  |    || ||||  ||   | |       |  |   |    | | ||||   ||||  | |  | | |    |||    |   |                  
GGGCCTTCCGGCCAAGAATCTCATGGCGGAGCGGCGACGGCGGAAGAAGCTTAATGATCGCTTGTACATGCTTCGCTCGGTGGTCCCCAAAATTACAAAGgtgagtactttcaaaccactcgggcaacttggcattc--actcgcccgctcctctttccatgcctttacctctttttctcctctcgctctcactcacactcaacttggtttgattttgtcag

upper sequence: GLYMA19G27480.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ15029 (Selaginella moellendorffii), 5'ss of exon 1
GGGGCTGCCCGCCAAGAATCTCATGGCGGAGAGGCGCCGCCGGAAGAAGCTCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAGgtatgactaacaaaaaccacaaaatttggttttggaaataat-tatttattaactgttggtcattactggttttgtttcaatgtttgttctcttgttgttc
     |||| ||||||||| |  ||||||||||||| || |||||||||||||| ||| |  | ||||||||  | || || || |||||||| | |||||| |  ||        | ||       | || ||| || ||| |   |  ||||  | | ||       | |||| |||   |                  
----ATGCCGGCCAAGAATTTGCTGGCGGAGAGGCGGCGGCGGAAGAAGCTCAACGATCGCCTCTACATGCTTCGATCGGTGGTGCCCAAGATCACCAAGgt-tctctcttgtctgctacg------gtttatgggaagaatgtgggtgctaac-atcgatcgc-----gctttgattcgcag------------------

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|298178876|gb|HO024611.1|HO024611
EST:     TCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAG                         ATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTG
genomic: TCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAGgtatgactaa ... ttgttggtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTG
EST: gi|23730171|gb|BU763190.1|BU763190
EST:     TCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAG                         ATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTG
genomic: TCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAGgtatgactaa ... ttgttggtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGGCTGCCCGCCAAGAATCTCATGGCGGAGAGGCGCCGCCGGAAGAAGCTCAATGATAGGTTGTACATGCTCAGGTCTGTTGTCCCCAAGATTAGCAAGgtatgactaacaaaaaccacaaaatttggttttggaaataattatttattaactgttggtcattactggttttgtttcaatgtttgttctcttgttgttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaataa