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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtag

Basic information

species Zea mays
transcript GRMZM2G104373_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 5'ss of exon 2
CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctgattccttgagg----acagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtag
||| || |||||||||||||||||||||||||| || |||||||| |||||||| ||| |||||||||||||||| ||||| ||||||||||| ||||||||||||     || |||  |       |||    | ||   || |  |  || |      ||   |||||| |||||  ||| |   || | || |||  |                                                                                          
CTTGACTCATCCTGAGCTATATGAGGACATTGGAATAAGGCCTCCCAAGGGAGTAATATTATATGGGGAACCTGGCACAGGCAAAACTCTACTTGCAAAGgtttgtctctttttcttaggacattgaagtcttgaattcccatgtttactccatttcaaattcaattcattaataaactagtaacttaa-taaatgctagt------------------------------------------------------------------------------------------

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 2
CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtag
| | || |||||||| |||||||| |||||||| |||| |||||| ||||| || ||  ||||||| ||||||||||| ||||| ||  | || || |||||||||| | ||   |||       |    || | || |      |  | |     |  | || | |          |   | |      |  |||      |  ||      || | | |  ||    | | ||  || |                                              
CCTGACGCATCCTGAACTATATGAAGACATTGGTATCAAGCCTCCTAAGGGGGTCATTTTATATGGAGAACCTGGAACTGGGAAGACATTGCTTGCGAAGgtttgtgtttatcttttgct--tcttctagagctgttttaatagagtttcaacatctcctttttactatctttatcttttggcagtgtttcaatttaaggagtgtttcagcatctta-agactatgccttttgtgtattcag---------------------------------------------

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA10G04920.1 (Glycine max), 5'ss of exon 2
CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtag
| | ||||||||||| |||||||| |||||||| |||| |||||| ||||| || ||  ||||||| |||||||| || ||||| ||  | || || ||||||||   | ||   |   |     |    || | || |      |  | ||    |  | || | |          | | | |       | |||      |  |       || | | |  ||    | | ||  || |                                              
CCTGACACATCCTGAACTATATGAAGACATTGGTATCAAGCCTCCTAAGGGGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcatttatcttt---gcttcttctagagctgttttaatagagtttcagcatctcctttttactacctttatctttaggcagtgttttgatttaaggagtgttccagcatctta-agacaatgccttttgtgtattcag---------------------------------------------

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA19G35510.1 (Glycine max), 5'ss of exon 2
CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctgattccttgaggacagttccaagtttttatt---tccatgccttagttgttttt-gttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtag
| | || |||||||| || ||||| |||||||| |||| |||||| |||||||| ||  |||| || ||||||||||| ||||| ||  | || || ||||| ||     |||  ||| ||    ||  | |     ||    |  |  ||| |  |||||||  ||| |   |    | ||  |  |||     | ||   ||                                                                                       
CCTGACGCATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgc----attttttggggtttcttatatggggcgatggaatataatcctgacatgttttttattcctcattttctctgtttaataacatggagtttgaaat---------------------------------------------------------------------------------------

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 2
CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgct------gattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtag
| | ||||||||||| || ||||| |||||||| |||| |||||| |||||||||||  ||||||||||||| ||||| ||||| ||  | || |||||||| ||   |      | || |||       |||  ||  | ||||   |||   ||   | ||| |  |  |  ||     | |        ||||    |||                                                                                          
CCTGACACATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTTATTTTATATGGGGAACCAGGAACTGGGAAGACATTGCTTGCAAAGgtgtgcattttttggggtttcttatatggtgttgaaatatattatcaacatatttt--ctatttctcattttctatgtt-taatacgaagtttgaatttcttt------------------------------------------------------------------------------------------

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 2
CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtag
  ||||||||||||| || |||||||||||||| |||| |||||| ||||| || ||||||||||| || ||||||||||| || ||  | || |||||||| |||  | ||   |        | | |    | | |      ||| |||    ||| | | |  |  || | |  |||  |  |    | |||||   | |  ||||  |                                                                           
TCTAACACATCCTGAACTGTATGAGGACATTGGTATCAAGCCTCCTAAGGGGGTCATACTATATGGAGAGCCTGGAACAGGAAAGACCTTGCTTGCAAAGgtgtgtattcatattt--------gcttc---ctatcaaactggtgcatta-caatttatctgccattttatatctctgattgtgccatcctctttttcctttcattttggt---------------------------------------------------------------------------

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtag
 || |||||||| ||||| ||||| |||||||| |||| ||| || |||||||||||  | ||||| ||||| || || ||||||||||| || || |||||   | | | ||     |||       || ||  || ||  | ||| |   |||| | ||| ||  ||        |     |||     |   ||  ||                                                                                      
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatac-gtttggcaaagggtgagatcatgtaattcttgacttgc-taccttgtctctgtacagagaagttctgctttgctaacaaggtgacctttgttg-------------------------------------------------------------------------------------

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ32659 (Selaginella moellendorffii), 5'ss of exon 2
CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtag
  | || ||||| ||||| || ||||||||||| ||||  ||||| |||||||| ||||| ||||| ||||||||||| || ||||| || || ||||||||   ||     || |||| |   || | |  |  | |||  |  || || ||| |                                                                                                                                   
ACTTACGCATCCGGAGCTGTACGAGGACATTGGAATCAAACCTCCCAAGGGAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaaatgtgacatctttgaag---gtgctacttcgtaattaactagctttggttctacag-------------------------------------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 2
CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtag
  | || ||||| ||||| || ||||||||||| ||||  ||||| |||||||| ||||| ||||| ||||||||||| || ||||| || || ||||||||  |||     || || | |   || |    |  | | |  |  || || ||| |                                                                                                                                   
ACTTACGCATCCAGAGCTGTACGAGGACATTGGAATCAAACCTCCCAAGGGAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaagtgtgacatcttttaag---gtgctgcttcgtaactaactagctttggttctacag-------------------------------------------------------------------------------------------------------------------------------

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|71318158|gb|DR795841.1|DR795841
EST:     GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAG                         GCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTT
genomic: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTT
EST: gi|148934976|gb|EC879019.2|EC879019
EST:     GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCG-AAAG                         GCTGTTGCCCATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
genomic: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
EST: gi|61117980|gb|DN558941.1|DN558941
EST:     GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAG                         GCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
genomic: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
EST: gi|60357188|gb|DN224161.1|DN224161
EST:     ATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAG                         GCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
genomic: ATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
EST: gi|61117979|gb|DN558940.1|DN558940
EST:     GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAG                         GCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
genomic: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
EST: gi|149110575|gb|EE190490.2|EE190490
EST:     GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAG                         GCTGTTGCCAATTCTACTTCAGCAACGTTCTTG
genomic: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTG
EST: gi|61117978|gb|DN558939.1|DN558939
EST:     GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAG                         GCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
genomic: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
EST: gi|32831887|gb|CD971565.1|CD971565
EST:     GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAG                         GCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA
genomic: GAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 128

CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 208

CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 231

CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 194

CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctg ... aacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG