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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaaaaataaacatgtgccattgtgttatcttaatgctgctgttgggataaagtaattatctctaattactgtatggtgtag

Basic information

species Glycine max
transcript GLYMA09G01820.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G01820.3 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 3
CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaaaaataaacatgtgccat-tgtgtta-tcttaatgctgctgttgggataaagtaattatctctaattactgtatggtgtag-----------
||||| || ||||||||||| |||||||| |||||||| |||||||| ||||| || |||||||| ||||||||||| |||||  ||||  |||| | || || |||      | ||  | | | ||  |     | |||   |    ||| | | |  |||||   |   |  | |           
CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAGgtcagtagcagaacaatcatcctttgtatgcatcaatttttttatatatattgtttttttataactgtatg-aattataatccagaattgcacaggcattg

upper sequence: GLYMA09G01820.3 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g50050.1 (Oryza sativa), 5'ss of exon 4
CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgt--agaaaaataaacatgtgc-cattgtgttatcttaatgctgctgttgggataaagtaattatctctaattactgtatggtgtag------------
|||||||| |||||||| ||||||||||| || ||||||||||| || || || || ||  | || || ||||||||  | ||||||||||||  || |  || ||| ||| | ||| |   | || |  || | ||||   |||     | |  | |  || |  | |    ||||             
CTTCAGGCCTATTTTCTGGTTCTTGATGATATAATGGATAACTCACAAACTCGACGAGGAAAACCCTGTTGGTTTAGGCTTCCCAAGgtttgtcaagtaggattaacttgtccacatagaaatgtccttgtgttactgt--agattctcgagtgttgttaaaatgttatg-attgtactccaactaaaca

upper sequence: GLYMA09G01820.3 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g50050.2 (Oryza sativa), 5'ss of exon 3
-------------CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgt--agaaaaataaacatgtgc-cattgtgttatcttaatgctgctgttgggataaagtaattatctctaattactgt-atggtgtag----------
             |||||||| |||||||| ||||||||||| || ||||||||||| || || || || ||  | || || ||||||||  | ||||||||||||  || |  || ||| ||| | ||| |   | || |  || | ||||   |||     | |  | |  || |  | | || ||              
GAGTAACCTGCAGCTTCAGGCCTATTTTCTGGTTCTTGATGATATAATGGATAACTCACAAACTCGACGAGGAAAACCCTGTTGGTTTAGGCTTCCCAAGgtttgtcaagtaggattaacttgtccacatagaaatgtccttgtgttactgt--agattctcgagtgttgttaaaatgttatgattgtactccaactaaaca

upper sequence: GLYMA09G01820.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G098569_T01 (Zea mays), 5'ss of exon 3
CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttg--tagaaaaataaacatgtgccatt----gtgttatcttaat--gctgctgttgggataaa-gtaattatctctaattactgtatggtgtag---
||||| || ||||||||||| |||||||| |||||||| ||||| || ||||| || |||||||| |||||||||||||||||  ||||| |   || |   |  |    |   | |       |||| |  ||    |  || |  |||    ||| | |    ||    ||   | | | ||   
CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAGgttagatcaggagcgtctatcctttttacttaccaaattatttctattgattcttgctttgatggctgtactaagtcttacactctcacttgggaagttt

upper sequence: GLYMA09G01820.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 3
CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaaaaataaacatgtgccattgt-------gttatcttaat--gctgctgttgggataaa-gtaattatctctaattactgtatggtgtag--
||||| || ||||||||||| |||||||| |||||||| ||||| || ||||| || ||||| || |||||||||||||||||  ||||| |   | ||  |   ||      ||          |||| |  ||    |  ||||  |||    ||| | |  ||| |      ||     ||   
CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAGgttagatcagaagcatctatccttttttacttaccaaattatttctatcaattcttgttttgatggttgtactaaggtcttacactcttacttgataagt

upper sequence: GLYMA09G01820.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G168681_T01 (Zea mays), 5'ss of exon 4
CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgt----agaaaaataaacatgtgccattgtgttatctta-atgctgctgttgggataaagtaattatctctaatta-ctgtatggtgtag-----------------------------
|||||||| |  |||||||| |||||||| || |||||| |||||||||| || ||||||||||| |||||||| || |||||  ||||| ||       || |  ||    |  |  ||| || ||     ||  | |  |  | |  ||  |  || || ||||  || | |   ||                               
CTTCAGGCTTTCTTTCTTGTGCTTGATGATATCATGGATGACTCTCACACTCGTCGCGGCCAGCCTTGCTGGTTCAGGGTGCCTCAGgttagtcttactgaataccaaagcatttctctgttttttcccctgtgtagttacttcggtgcagagaa-atttcgaattctctttttcaagtgatagctaagggtggatttcgtttgaaatag

upper sequence: GLYMA09G01820.3 (Glycine max), 5'ss of exon 4
lower sequence: AT5G47770.1 (Arabidopsis thaliana), 5'ss of exon 4
CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaaaaataaacatgtgccattgtgttatcttaatgctgctgttgggataaagtaattatctctaattactgtatggtgtag
|| || || ||||| ||||| |||||||| |||||||||||||||  ||| ||||| || || || |||||||| ||||| ||  ||||       ||| |   ||| |         || |  | | ||||| ||    |  |    ||| |  |  | |  |  |        
CTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAGgt-------aaagttttcatat---------tttttgtcacgctgcagtc--cactagactattctaacacaatgttacag-------

upper sequence: GLYMA09G01820.3 (Glycine max), 5'ss of exon 4
lower sequence: Vv19s0015g01010.t01 (Vitis vinifera), 5'ss of exon 4
CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgt------ttgtagaaaaataaacatgtgccattgtgttatcttaat----gctgctgttgggataaagtaattatctctaattactgta----tggtgtag
||||| |||||||| ||||| |||||||| |||||||||||||| || ||||| || || || || |||||||| || || ||||||||       | |||  |        |     |  |||  | | |  |      |||   |  |||||||| |  |   |||| |    ||    ||   |||
CTTCAAGCATATTTCCTTGTGCTTGATGATATTATGGATAACTCGCATACACGTCGAGGTCAACCTTGCTGGTTCAGGGTTCCCAAGgtgcaagcctatagtgaccctttttttctttacagtgcaagcatgtttgcaattgccactttgataaagtga--agtactaactttcttagatttgtcttag

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|13180801|gb|BG352141.1|BG352141
EST:     ATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCGACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|192297466|gb|FG992694.1|FG992694
EST:     ATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|193645084|gb|FK593384.1|FK593384
EST:     ATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAA
genomic: ATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAA
EST: gi|192325137|gb|FK017523.1|FK017523
EST:     ATAACTCTCACACACGCCGCGGCCAGCCATACTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|6567264|gb|AW234875.1|AW234875
EST:     ATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|7028813|gb|AW458596.1|AW458596
EST:     ATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|8826734|gb|BE210464.1|BE210464
EST:     ATAACTCTCACACACACCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|213591397|gb|DB973830.1|DB973830
EST:     ATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
EST: gi|207755571|gb|GD726624.1|GD726624
EST:     ATAACTCTCACACACGTCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG                         GTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA
genomic: ATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaa ... tatggtgtagGTTGGAATGATTGCAGCCAATGATGGAGTTCTACTAAGAAACCATATTCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAGgtttgtagaaaaataaacatgtgccattgtgttatcttaatgctgctgttgggataaagtaattatctctaattactgtatggtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG