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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATACATTGAAGAAACTTATGGAAGTTGGGCAGTGTTCCGGCCACAGTACATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaactttcttaaacaaacgttattattaactttaaatacatatgaagccttgtttcaataaagtgaagtgctaacaacacactctctaacatg...

Basic information

species Glycine max
transcript GLYMA10G03200.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G03200.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os07g11110.1 (Oryza sativa), 5'ss of exon 4
AAATACATTGAAGAAACTTATGGAAGTTGGGCAGTGTTCCGGCCACAGTACATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggg-----gaactttcttaaacaaacgttattattaactttaaata--catatgaagccttgtttcaataaagtgaagtgctaacaacacactctctaacatg
|| ||||| |  ||    |  || || |||||   ||||||||| ||||||||||| || || ||||||||||| ||||| ||||||||||| || ||||||||         ||    |  || ||||   |   |  || || |||    |  |   | | || ||  | |  |    |    |  |||     |  ||      
AAGTACATCGCGGAGCAGTTCGGCAGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaaaatcacccaaatccccccaaccaaattctccca--aatttcaaaccgccccaaacaacattcttcaatttgaagacaaaattgtcaatttttttactg-----

upper sequence: GLYMA10G03200.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G111216_T01 (Zea mays), 5'ss of exon 4
AAATACATTGAAGAAACTTATGGAAGTTG---GGCAGTGTTCCGGCCACAGTACATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaactttcttaaacaaacgttattattaactttaaatacatatgaagccttgtttcaataaagtgaagtgctaacaacacactctctaacatg---
   ||||| |  ||    |  || || ||   |||   ||||||||| ||||||||||| || || ||||||||||| ||||| ||||||||||| || ||||||||            ||||||  |   |   ||   || |    |||      |||   |||    | |   |   | | |  ||   ||  |  ||||   
---TACATCGCGGAGCAGTTCGGCAGCTGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaa------------taaacagcc--cagccttggattcattctcattattctcctctcttctccgacgaccatgacgacctccatggtccgtc-catgcag

upper sequence: GLYMA10G03200.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G63140.1 (Arabidopsis thaliana), 5'ss of exon 4
AAATACATTGAAGAAACTTATGGAAGTTGGGCAGTGTTCCGGCCACAGTACATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaactttcttaaacaaacgttattattaactttaaatacatatgaagccttgtttcaataaagtgaagtgctaacaacacactctctaacatg
|| ||| | |  ||||| |  || |  |||||    || || || ||||||||||| || |||||||||||||||||||| || || ||||| || ||| |||||      | ||| | |||  |     | | || |  ||| |||    || |      |   | || ||   | | |                    
AAGTACTTAGCCGAAACATTCGGGAACTGGGCCTCCTTTCGACCGCAGTACATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaag------tctctcacacacccaaagatttcaa-tacaaagaca---aaaacacgtaatggttgaaatgtgttcccag-------------------

upper sequence: GLYMA10G03200.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv07s0104g00510.t01 (Vitis vinifera), 5'ss of exon 4
AAATACATTGAAGAAACTTATGGAAGTTGGGCAGTGTTCCGGCCACAGTACATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaactttcttaaacaaacgttattattaactttaaatacatatgaagccttgtttcaa-taaagtgaagtgctaacaac-acactctctaacatg
| |||||||  |||   ||  || || |||||| | ||||| || |||||||||||||| ||||| ||||||||||| |||||||||||||| |||||| ||||| | ||    |||   ||   ||| | |     ||  || |||  || |  | | ||  || |    ||   |  | |||   |  | |||| |   |
ACATACATTTCAGAGGTTTTCGGCAGCTGGGCAATTTTCCGTCCGCAGTACATGATTGGATCTGGAAACAACAAAGATTGTGAGGAGTGGTTCTTTGACCgtaagcg-aataaccttgcgcattggtt-tgaactttttgtaacacagctgcattcatcttcaaaatcccctgccattttcacattgatccgctctgaacag

upper sequence: GLYMA10G03200.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ07654 (Selaginella moellendorffii), 5'ss of exon 4
AAATACATTGAAGA-AACTTATGGAAGTTGGGCAGTGTTCCGGCCACAGTACATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaactttcttaaacaaacgttattattaactttaaatacatatgaagccttgtttcaataaagtgaagtgctaacaacacactctctaacatg
  | |  |  |||    |||       |||| |   |||  | ||||||||||||| ||| || || |||||||| ||||| ||||| |||||||| |||||||||     | | |||        |||   |   |   | || || | |    |                                             
-TACATTTCAAAGTCGGCTTTCAAGTTTTGGTCCTCGTTTAGACCACAGTACATGACTGGCTCCGGGAACAACAAGGACTGCGAGGAATGGTTTTTCGACAgtaagtttttcctccttcctttcgtgtttcaagggatcatgaaaacgttttggacag-------------------------------------------

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|120529998|gb|EH258132.1|EH258132
EST:     CATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACA                         GGATTGTTCGGGACAGACCTGTGCCAATTCCTGGCTCGGGACTGCAACTCA
genomic: CATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaa ... atatttgtagGGATTGTTCGGGACAGACCTGTGCCAATTCCTGGCTCGGGACTGCAACTCA
EST: gi|20498478|gb|BQ273408.1|BQ273408
EST:     CATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACA                         GGATTGTTCGGGACAGACCTGTGCCAATTCCTGGCTCGC-ACTGCAACTCA
genomic: CATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaa ... atatttgtagGGATTGTTCGGGACAGACCTGTGCCAATTCCTGGCTCGGGACTGCAACTCA
EST: gi|8669439|gb|BE190546.1|BE190546
EST:     CATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACA                         GGATTGTTCGGGACAGACCTGTGCCAATTCCTGGCTCGGGACTGCAACTCA
genomic: CATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaa ... atatttgtagGGATTGTTCGGGACAGACCTGTGCCAATTCCTGGCTCGGGACTGCAACTCA
EST: gi|209729821|gb|BW658626.1|BW658626
EST:     CATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACA                         GGATTGTTCGGGACAGACCTGTGCCAATTCCTGGCTCGGGACTGCAACTCA
genomic: CATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaa ... atatttgtagGGATTGTTCGGGACAGACCTGTGCCAATTCCTGGCTCGGGACTGCAACTCA
EST: gi|7639890|gb|AW734203.1|AW734203
EST:     CATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACA                         GGATTGTTCGGGACAGACCTGTGCCAATTCCTGGCTCGGGACTGCAACTCA
genomic: CATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaa ... atatttgtagGGATTGTTCGGGACAGACCTGTGCCAATTCCTGGCTCGGGACTGCAACTCA
EST: gi|22928688|gb|BU545827.1|BU545827
EST:     CAACAAAGACTGTGAGGAGTGGTTTTTTGACA                         GGATTGTTCGGGACAGACCTGTGCCAATTCCTGGCTCGGGACTGCAACTCA
genomic: CAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaa ... atatttgtagGGATTGTTCGGGACAGACCTGTGCCAATTCCTGGCTCGGGACTGCAACTCA
EST: gi|20814787|gb|BQ299265.1|BQ299265
EST:     CATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACA                         GGATTGTTCGGGACAGACCTGTGCCAATTCCTGGCTCGGGACTGCAACTCA
genomic: CATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaa ... atatttgtagGGATTGTTCGGGACAGACCTGTGCCAATTCCTGGCTCGGGACTGCAACTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATACATTGAAGAAACTTATGGAAGTTGGGCAGTGTTCCGGCCACAGTACATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaactttcttaaacaaacgttattattaactttaaatacatatgaagccttgtttcaataaagtgaagtgctaacaacacactctctaacatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactctct