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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcatggtagtaatgttgtgcacttgcactatatacagatacactgttgtgagttgtgacatagtaccgctgataattttcttctatcatt...

Basic information

species Zea mays
transcript GRMZM2G382240_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G382240_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g42320.4 (Oryza sativa), 5'ss of exon 7
--------------GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGG-AAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcatggtagtaatgttgtgcacttgcactatatacagatacactgttgtgagttgtgacatagtaccgct------gataattttcttctatcatt--------------------------------------------------
              |||||||||||||||||||||||||||||||| |||||||| ||||| |||||||| || ||||||||||||||||||||||| |||||||||   |     || || |||  || |||  |||| | |     | || | |  | ||   | |  | |    | |      ||||  ||  ||| |   ||                                                  
TATTATTTCTACAGGTTGATCCCTCAGGATCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTCTCCAATGCAAAGACATTTCTTGAAAAAAGgtacatagcataccactaatattgtattgtact-acactctgttttcct-caatctgatcagaaataaagtggatttgtttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcag

upper sequence: GRMZM2G382240_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 7
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGG-AAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcatggtagtaatgttgtgcacttgcactatatacagatacactgttgtgagttgtgacatagtaccgct------gataattttcttctatcatt--------------------------------------------------
|||||||||||||||||||||||||||||||| |||||||| ||||| |||||||| || ||||||||||||||||||||||| |||||||||   |     || || |||  || |||  |||| | |     | || | |  | ||   | |  | |    | |      ||||  ||  ||| |   ||                                                  
GTTGATCCCTCAGGATCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTCTCCAATGCAAAGACATTTCTTGAAAAAAGgtacatagcataccactaatattgtattgtact-acactctgttttcct-caatctgatcagaaataaagtggatttgtttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcag

upper sequence: GRMZM2G382240_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA15G41330.1 (Glycine max), 5'ss of exon 9
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGG-AAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcatggtagtaatgttgtgcacttgcactatatacagatacactgttgtgagttgtgacatagtaccgctgataattttcttctatcatt-----
|| ||||| ||||| ||||| || || ||||| || || || ||||| |||||||| || ||||||||||| |||||||| ||||||||     |       ||| |  ||| ||||     | | | |  || | ||    | |   |||||   | ||  |  | ||    |    ||   |       
GTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACGTTTCTTGAGAAGAGgtaagcttttcatcaatagca--gttctgcaagcaaaatgtgtggag-tgcatcaattttttttgtgt--ttgtgtccattatgtgctgtggctggtaccccttg

upper sequence: GRMZM2G382240_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA01G25940.2 (Glycine max), 5'ss of exon 8
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGG-AAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcatggtagtaatgttgtgcacttgcactatatacaga-tacactgttgtgagttgtgacatagtaccgctgataattttcttctatcatt
|| ||||| || || ||||| || || ||||| || || || ||||| |||||||| || ||||||||||| |||||||| ||||||||     |       ||||| |  ||   |     |  || |    | |  |      |  ||| |    | ||  |  | ||    |    |   ||  
GTGGATCCATCGGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAGgtaagcttttcatcaatagtagttctgca-agcaaaagcatgtgtgaagtgaatcagaatttgtttttgtgttgtgtccattatgtgctgtggcccacacc

upper sequence: GRMZM2G382240_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA03G16660.1 (Glycine max), 5'ss of exon 9
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGG-AAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcatggtagtaatgttg-tgcacttgcactata--tacagatacactgttgtgagttgtgacatagtaccgctgataattttcttctatcatt
|| ||||| ||||| ||||| || || ||||| || || || ||||| |||||||| || ||||||||||| |||||||| |||||||| |||   |  | ||     | ||  ||||  |   ||     |||  | | |      ||  |     | |   |  | ||  |||||| |  | |    
GTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACTTTTCTTGAGAAGAGgtaaatagatttgtcgtgtcttttttaatgcatctcttcttcccttaccaaaaaaaaaggatgcatatcttcttcaaaa-gttgtcaattttgtggtttgg--

upper sequence: GRMZM2G382240_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA08G17810.3 (Glycine max), 5'ss of exon 9
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGG-AAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcatggtagtaatgttgtgcacttgcactatatacagatacactgttgtgagttgtgacatagt-----accgctgataattttcttctatcatt
|| ||||| ||||| ||||| || || ||||| || || || ||||| |||||||| || ||||||||||| |||||||| ||||||||     |      |||  | |  |     |    || || |  || | ||      |  ||||||   ||       |   ||||| |  |   ||| |    
GTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACGTTTCTTGAGAAGAGgtaagcttttcatcagtaacagttcttcaagcaaaaac-atgtggag-tgcatcaaaatttgttgtgttgtatccattaagtactgatgaaatctgtctgtg---

upper sequence: GRMZM2G382240_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 5'ss of exon 8
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAA-AATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgta-------cataatctcatggtagtaatgttgtgcacttgcactatatacagatacactgttgtgagttgtgacatagtaccgctgataattttcttctatcatt
|| ||||| ||||| ||||| ||||| ||||| || || || ||||| || ||||| ||||||||||||||||||||||| ||||||||       || ||| |  | |  ||    || |  | |   |  |   |       |   || |    | ||| |   |  |    | |||||| ||        
GTGGATCCATCAGGTTCATATTTCTCATGGAAAGCCTCCGCAATGGGGAAGAATGTCTCAAATGCAAAGACATTTCTTGAGAAGAGgtatttaaatcagaatttggttgctgtgtctttttaaaatgatatcaagcagcagcctatctttattgtgtttgatacttttgcaacaacaattttttta-------

upper sequence: GRMZM2G382240_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S61_202V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGG-AAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatct-catggt-agta-atgttgtgcacttgcactatatacagataca-ctgttgtgagttgtgacatagtaccgctgataattttcttctatcatt----------------------------
|| ||||| |||||||| |||||||| |||||||||||||| || || || |||||||| ||||| ||||| || || || || ||||   | |||| |||  |  | | || ||||        ||| ||| | | |||| |  |  | |||||  |||   | ||     ||| |    |   | | |                            
GTGGATCCTTCAGGATCGTACTTCTCATGGAAGGCATCAGCAATAGGCAAGAATGTGTCCAATGCCAAGACTTTCCTAGAGAAAAGgtcagtcatcttcatacttggcacatattgtctttcataactttat-ccgttacatccatgataagttg--acaagtttccatatgtaactcgaattggtgacttattcactgggttcttctgttcaagcag

upper sequence: GRMZM2G382240_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S2_595V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGG-AAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcatggtagtaatgttgtgcacttgcactatatacagatacactgttgtgagttgtgacat-agtaccgc-tgataattttcttctatcatt----------------------------------------------
|| ||||| ||||||||||||||||| |||||||||||||| || || || |||||||| ||||| ||||| ||  | || || ||||   |  | ||      ||     | ||   | | | | | ||    |||  ||| ||    ||    || |||   |   || |   ||| | |   |||                                              
GTAGATCCATCAGGATCATACTTCTCATGGAAGGCATCAGCAATTGGCAAGAATGTGTCTAATGCGAAGACTTTCTTAGAGAAAAGgtcggtcctttc-catacgttgcactctgttttcg-attctgta-gtctacgatgtggtagaatgcaggatgagttttgaacgagacgattcgtgtcatatttaatatgagatagtgactcattcgagaggcatactgttacaagcag

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|6851609|gb|AW352619.1|AW352619
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGG-AAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|211467417|gb|FK984374.1|FK984374
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGG-AAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|29543478|gb|CB605564.1|CB605564
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGG-AAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|6993991|gb|AW453205.1|AW453205
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGG-AAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|6828067|gb|AW331710.1|AW331710
EST:     TCAGCCATGGGAAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAG                         ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGG-AAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatc ... ttcattgtagATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAAAAGAGgtacataatctcatggtagtaatgttgtgcacttgcactatatacagatacactgttgtgagttgtgacatagtaccgctgataattttcttctatcatt

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