Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttcttgttagagctgacaatctgagttctttttttttcatccaagtccttattctcttaatgattggtctgataacacatcaattgcttttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG

Basic information

species Zea mays
transcript GRMZM2G070315_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070315_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g10650.1 (Oryza sativa), 3'ss of exon 2
ggttcttgttagagctgacaatctgagttctttttttttcatccaagtccttattctcttaatgattggt--ctgataacacatcaattgcttttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG
  || |    | |  | |  ||      | |||||| ||  ||  |   | |  | |||  |    || |  |||| ||||  | || | || ||  | ||||||||||| |||||||| || |||||||||||  | |||||||||||||||||| |||
--ttgtcacaacaattcattatgcactctgttttttcttagtctgaaaacctgatatctccacagctgatgactgacaacatctgaactactgttgctacagGAACCATTCGTCAACATCCCTGACGACAAAATTCGAGAGGCGCTCAAAGTTGTCCTAG
















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|211207266|gb|FK949980.1|FK949980
EST:     TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAG                         GAACCATTTGTCAACATACCCGACGACAAAATAAG
genomic: TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAG
EST: gi|32925414|gb|CF030226.1|CF030226
EST:     TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAG                         GAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|149028367|gb|EE286122.2|EE286122
EST:     TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAG                         GAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|148939874|gb|EC884586.2|EC884586
EST:     TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAG                         GAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|88755665|gb|DY539806.1|DY539806
EST:     AGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAAG                         GA-CCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGT
genomic: AGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAA-Ggtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGT
EST: gi|89758678|gb|DY687773.1|DY687773
EST:     TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAG                         GAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|211209829|gb|FK949987.1|FK949987
EST:     TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAG                         GAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|148937447|gb|EC881628.2|EC881628
EST:     TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAG                         GAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|148940906|gb|EC885740.2|EC885740
EST:     TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAG                         GAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|149028366|gb|EE154635.2|EE154635
EST:     TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAG                         GAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|149083277|gb|EE172563.2|EE172563
EST:     TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAG                         GAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
EST: gi|211207269|gb|FK949983.1|FK949983
EST:     TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAG                         GAACCATTTGTCAACATACCCGACGACAAA
genomic: TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAA
EST: gi|76290784|gb|DV030352.1|DV030352
EST:     TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAG                         GAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT
genomic: TAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTT

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: 44 (upstream exon), 43 (downstream exon)
Score: 19

GTACCTGTGCCCGGAGCCGTACCCGGGGACGAACACGGAGTTCCTAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

GTACCTGTGCCCGGAGCCGTACCCGGGGACGAACACGGAGTTCCTAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 59

GTACCTGTGCCCGGAGCCGTACCCGGGGACGAACACGGAGTTCCTAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 62

GTACCTGTGCCCGGAGCCGTACCCGGGGACGAACACGGAGTTCCTAGAAAAGAATGGGATCAGGCTCCACCAGTTCGGAATCGAGGGGCGCAAGgtaaatccta ... tttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtccttattctcttaatgattggtctgataacacatcaattgcttttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG
                          tgataac  putative branch site (score: 62)
                                        ttgcttttttttc  putative PPT
                                      aattgctttttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttcttgttagagctgacaatctgagttctttttttttcatccaagtccttattctcttaatgattggtctgataacacatcaattgcttttttttcagGAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG

-gttcttg
- - - - - - -gctgaca
- - - - - - - - - - - - - - - - - - - -catccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacacat