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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcattgtagtaatgttgtgcacttgctctatatacagatacactgttgtgagttatgacatagtaccgctgataattttcttctgtcatt...

Basic information

species Zea mays
transcript GRMZM5G850355_T06
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G850355_T06 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g42320.4 (Oryza sativa), 5'ss of exon 7
--------------GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcattgtagtaatgttgtgcact-tgctctatatacagatacactgttgtgagttat---gacatagtaccgctgataattttcttctgtcatt--------------------------------------------------
              |||||||||||||||||||||||||||||||| |||||||| ||||| |||||||| || ||||||||||||||||||||||| |||||||||   |     || || |||  || |||   |||| | | |    |     |    | | |    ||  |  |  ||  ||||  ||  |||     ||                                                  
TATTATTTCTACAGGTTGATCCCTCAGGATCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTCTCCAATGCAAAGACATTTCTTGAAAAAAGgtacatagcataccactaatattgtattgtactacactctgttttcctcaatctgatcagaaataaagtggatttgtttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcag

upper sequence: GRMZM5G850355_T06 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 7
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcattgtagtaatgttgtgcact-tgctctatatacagatacactgttgtgagttatg---acatagtaccgctgataattttcttctgtcatt--------------------------------------------------
|||||||||||||||||||||||||||||||| |||||||| ||||| |||||||| || ||||||||||||||||||||||| |||||||||   |     || || |||  || |||   |||| | | |    |     |    | | | |   |  |  |  ||  ||||  ||  |||     ||                                                  
GTTGATCCCTCAGGATCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTCTCCAATGCAAAGACATTTCTTGAAAAAAGgtacatagcataccactaatattgtattgtactacactctgttttcctcaatctgatcagaaataaagtggatttgtttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcag

upper sequence: GRMZM5G850355_T06 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA15G41330.1 (Glycine max), 5'ss of exon 9
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcattgtagtaatgttgtgcacttgctctatatacagatacactgttgtgagttatgacatagtaccgctgataattttcttctgtcatt-----
|| ||||| ||||| ||||| || || ||||| || || || ||||| |||||||| || ||||||||||| |||||||| ||||||||     |       ||| |  ||| ||||       | | |  || | ||    | |   || ||   | ||  |  | ||    |    |||  |       
GTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACGTTTCTTGAGAAGAGgtaagcttttcatcaatagca--gttctgcaagcaaaatgtgtggag-tgcatcaattttttttgtgt--ttgtgtccattatgtgctgtggctggtaccccttg

upper sequence: GRMZM5G850355_T06 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G25940.2 (Glycine max), 5'ss of exon 8
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcattgtagtaatgttgtgcacttgctctatatacaga-tacactgttgtgagttatgacatagtaccgctgataattttcttctgtcatt
|| ||||| || || ||||| || || ||||| || || || ||||| |||||||| || ||||||||||| |||||||| ||||||||     |       ||||| |  ||    |     | || |    | |  |      |  ||| |    | ||  |  | ||    |    |   ||  
GTGGATCCATCGGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAGgtaagcttttcatcaatagtagttctgcaagcaaaagc-atgtgtgaagtgaatcagaatttgtttttgtgttgtgtccattatgtgctgtggcccacacc

upper sequence: GRMZM5G850355_T06 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA03G16660.1 (Glycine max), 5'ss of exon 9
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcattgtagtaatgttg-tgcacttgctctata--tacagatacactgttgtgagttatgacatagtaccgctgataattttcttctgtcatt
|| ||||| ||||| ||||| || || ||||| || || || ||||| |||||||| || ||||||||||| |||||||| |||||||| |||   |  | ||     | ||  ||||  |  |||     |||  | | |      ||  | ||    |   |  | ||  |||||| |  | |    
GTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACTTTTCTTGAGAAGAGgtaaatagatttgtcgtgtcttttttaatgcatctcttcttcccttaccaaaaaaaaaggatgcat-atcttcttcaaaagttgtcaattttgtggtttgg--

upper sequence: GRMZM5G850355_T06 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G17810.3 (Glycine max), 5'ss of exon 9
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcattgtagtaatgttgtgcacttgctctatatacagatacactgttgtgagttatgacatagt-----accgctgataattttcttctgtcatt
|| ||||| ||||| ||||| || || ||||| || || || ||||| |||||||| || ||||||||||| |||||||| ||||||||     |      |||  | |  |     |     | || |  || | ||      |  ||| ||   ||       |   ||||| |  |   |||||    
GTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACGTTTCTTGAGAAGAGgtaagcttttcatcagtaacagttcttcaagcaaaaac-atgtggag-tgcatcaaaatttgttgtgttgtatccattaagtactgatgaaatctgtctgtg---

upper sequence: GRMZM5G850355_T06 (Zea mays), 5'ss of exon 2
lower sequence: AT1G79210.3 (Arabidopsis thaliana), 5'ss of exon 9
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtac--ataatctcattgtagtaatgttgtgcacttgctctatatacagatacactgttgtgagttatgacatagtaccgctgataattttcttctgtcatt
|| ||||| || || || || ||||| ||||| || || || |||||||| ||||| || ||||||||||| |||||||| |||||||    ||||| |     | ||  || || |    || |||   |  |   |     ||     ||| | | | |  | |                      
GTGGATCCATCTGGCTCTTATTTCTCATGGAAAGCTTCTGCAATGGGAAAGAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAGgtgataataatttaccatttgtggtgatgagtttatgatct---tggaagcatgtcatttcatctta-gtctttgatcag----------------------

upper sequence: GRMZM5G850355_T06 (Zea mays), 5'ss of exon 2
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 5'ss of exon 8
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgta-------cataatctcattgtagtaatgttgtgcacttgctctatatacagatacactgttgtgagttatgacatagtaccgctgataattttcttctgtcatt
|| ||||| ||||| ||||| ||||| ||||| || || || ||||| || ||||| ||||||||||||||||||||||| ||||||||       || ||| |  |||  ||    || |  | |      |   |       |   || |    | ||| |   |  |    | |||||| ||        
GTGGATCCATCAGGTTCATATTTCTCATGGAAAGCCTCCGCAATGGGGAAGAATGTCTCAAATGCAAAGACATTTCTTGAGAAGAGgtatttaaatcagaatttggttgctgtgtctttttaaaatgatatcaagcagcagcctatctttattgtgtttgatacttttgcaacaacaattttttta-------

upper sequence: GRMZM5G850355_T06 (Zea mays), 5'ss of exon 2
lower sequence: PP1S61_202V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatct-cattgtagtaatgttgtgcacttgctctatata-cagataca-ctgttgtgagttatgacatagtaccgctgataattttcttctgtcatt----------------------------
|| ||||| |||||||| |||||||| |||||||||||||| || || || |||||||| ||||| ||||| || || || || ||||   | |||| |||  | |  |  |  ||   ||  |   | || | | |||| |  |  | ||||  ||||   | ||     ||| |    |  || | |                            
GTGGATCCTTCAGGATCGTACTTCTCATGGAAGGCATCAGCAATAGGCAAGAATGTGTCCAATGCCAAGACTTTCCTAGAGAAAAGgtcagtcatcttcatacttggcacatattgtctttcataactttatccgttacatccatgataagtt--gacaagtttccatatgtaactcgaattggtgacttattcactgggttcttctgttcaagcag

upper sequence: GRMZM5G850355_T06 (Zea mays), 5'ss of exon 2
lower sequence: PP1S2_595V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcattgtagtaatgttgtgcacttg-ctctatatacagatacactgttgtgagttatgacat-agtaccgc-tgataattttcttctgtcatt----------------------------------------------
|| ||||| ||||||||||||||||| |||||||||||||| || || || |||||||| ||||| ||||| ||  | || || ||||   |  | ||  |   ||     | ||   | |  ||| ||  |   |||  ||| ||    |     || |||   |   || |   ||| | |   |||                                              
GTAGATCCATCAGGATCATACTTCTCATGGAAGGCATCAGCAATTGGCAAGAATGTGTCTAATGCGAAGACTTTCTTAGAGAAAAGgtcggtcctttccatac-gttgcactctgttttcgattctgtagtc---tacgatgtggtagaatgcaggatgagttttgaacgagacgattcgtgtcatatttaatatgagatagtgactcattcgagaggcatactgttacaagcag

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|5762225|gb|AI967273.1|AI967273
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|211253078|gb|FL452731.1|FL452731
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACMCAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|5108080|gb|AI739793.1|AI739793
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|6020496|gb|AW065424.1|AW065424
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|4572854|gb|AI586503.1|AI586503
EST:     AAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: AAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|211302508|gb|FL360538.1|FL360538
EST:     GAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGG--ATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: GAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|211244646|gb|FL472888.1|FL472888
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|211246869|gb|FL472890.1|FL472890
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|6653876|gb|AW267281.1|AW267281
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|12967997|gb|BG264944.1|BG264944
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|5819357|gb|AI987563.1|AI987563
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|5525504|gb|AI861397.1|AI861397
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|5597152|gb|AI891355.1|AI891355
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGCCATTTCTTGAAAAGAG                         AT-CCCAGAGGATATGGAACTTGATGATGCCATCCCCCCTGCAATTTTGNC
genomic: TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|33093559|gb|CF053553.1|CF053553
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|32908068|gb|CF012881.1|CF012881
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTCGAGAAGAG                         ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|211246870|gb|FL472891.1|FL472891
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcattgtagtaatgttgtgcacttgctctatatacagatacactgttgtgagttatgacatagtaccgctgataattttcttctgtcatt

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