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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actctactgttcattctggaaggcattcttgtgataaccagttgtatagttttggtactattaaaacaacagtacatcttattatgctttcctaattcagCATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAGCATCGGAATACCGACCCGTGTCCAGACTGCCTTCCGTATGTCAGAAGTT

Basic information

species Zea mays
transcript GRMZM2G139462_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139462_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g73450.1 (Oryza sativa), 3'ss of exon 4
actctactgttcattctggaaggcat---tcttgtgataaccagttgtatagttt--tggtactat-taaaacaacagtacatcttattatgctttcctaattcagCATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAGCATCGGAATACCGACCCGTGTCCAGACTGCCTTCCGTATGTCAGAAGTT
    |  | |  |     |||| |||   || ||| ||||    ||  ||| |||    | |  |  ||   || || |  |||||| | |  ||||||||||||||||| |||| |||||||||||||| |||||||||||||| || ||||||||||| |||||||| ||||||||||| ||||| || |||||||||||||||
----tgttttaaaaaaaagaagacatcattcctgttataagtgatttcataatttctcagcataaaatagttcaccactttatcttactct--tttcctaattcagCATGTTGGCTACTGTGATGAATGCCATATTTCTTCAAGCAACAATGGAGAGCATTGGAATACCAACCCGTGTCCAAACTGCATTTCGTATGTCAGAAGTT

upper sequence: GRMZM2G139462_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G32340.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------------------actctactgttcattctggaaggcattcttgtgataaccagttgtatagttttggtactattaa-aacaacagtacatcttattatgctttcctaattcagC-------ATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAGCATCGGAATACCGACCCGTGTCCAGACTGCCTTCCGTATGTCAGAAGTT
                                                                                 | | |  || ||| ||     ||| |     |     |||||   |   |   |   |  |  |  | |    | | ||| ||   ||   ||||| | |       ||| |||||||||| ||||||||||||||||||||||| || ||||| || || || || || || || || |||||||| || |||||||| || |||
gtgattcccttaatctcttaatttttatcttgaaggttaagtcagggcactgatcgctgatgtgctggttgttaacttagatttccaatttattatgatccacatccactatactttgagttgctcaaaatgcatgagagaagtagtatccaggctttttactaattttgtttaatttatcctctagGATGTTGGCCACTGTTATGAATGCTATATTTCTTCAAGCAACAATGGAAAGTATTGGCATTCCTACTCGGGTGCAGACTGCATTTCGTATGTCTGAGGTT

upper sequence: GRMZM2G139462_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G15610.1 (Glycine max), 3'ss of exon 4
actctactgttcattctggaaggc-attcttgtgataaccagttgtatagttttggtactattaaaaca-acagtacatcttattatgctttcctaattcagCATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAGCATCGGAATACCGACCCGTGTCCAGACTGCCTTCCGTATGTCAGAAGTT
  | | |  || ||| ||     | || |||    |  |      |  |      ||| |||  |  |  |      || || ||    ||  |   |  || ||| |||||||||| ||||||||||||||||||||||| || |||||||| || || || || || || || ||||| || || |||||||| || |||
catttccaatttattatgatccactatgctttgagttgctcaaaatgcatgagaagtagtatccaggcttattactaattttgtttaatttatcc--tctagGATGTTGGCCACTGTTATGAATGCTATATTTCTTCAAGCAACAATGGAGAGTATAGGCATTCCTACTCGGGTGCAGACCGCATTTCGTATGTCTGAGGTT

upper sequence: GRMZM2G139462_T04 (Zea mays), 3'ss of exon 3
lower sequence: AT3G18680.1 (Arabidopsis thaliana), 3'ss of exon 4
---actctac-tgttcattctggaaggcattcttgtgataaccagttgtatagttttggtactattaaaacaacagtac---atcttattatgctttcctaattc----agCATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAGCATCGGAATACCGACCCGTGTCCAGACTGCCTTCCGTATGTCAGAAGTT
   |   |||   ||  |     | |   ||||| |  | ||  |  | | |       |  |  |  |      ||      ||| |||    | ||  || |     || |||||||| |||||||||||||| ||||||||||||||||| |||||||| || || || || |||||||| || ||||| ||||| ||||| ||||| 
gtaatcatacgcctttgtgtcaaaggatcttcttcttcttactcggagaagatccagaattttcctctactggaggtttttggtctcattggtttatctgaaattggatagGATGCTGGCAACTGTGATGAATGCAATATTTCTTCAAGCGACAATGGAGAGTATTGGCATCCCAACCCGTGTTCAAACTGCTTTCCGCATGTCGGAAGTC

upper sequence: GRMZM2G139462_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0044g00890.t01 (Vitis vinifera), 3'ss of exon 5
-actctact-gttcattctggaaggcattcttgtgata-accagttgtatagttttggtactattaaaacaacagtacatcttattatgctttcctaattcagCATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAGCATCGGAATACCGACCCGTGTCCAGACTGCCTTCCGTATGTCAGAAGTT
  ||  | | |    || |     | |  | |||  |  | |  |  |  | || ||  ||| |  ||      ||| | | | | ||| |    |  || || ||| |||| ||||| ||||||||||||||||||||||| || ||||||||||| || || || || |||||||||||||| ||||| ||||| ||||||
ttcttgattcgcgtgttgtatggaggacacctgttgtgtatctttccttaaattatgtaactgt--aatttggggtagaacct-tgatgttggaattttttagGATGTTGGCTACTGTTATGAATGCTATATTTCTTCAAGCAACAATGGAGAGCATTGGCATCCCAACTCGTGTCCAGACTGCATTCCGAATGTCTGAAGTT

upper sequence: GRMZM2G139462_T04 (Zea mays), 3'ss of exon 3
lower sequence: PP1S241_40V6.1 (Physcomitrella patens), 3'ss of exon 4
-----actctactgttcattctggaaggcattcttgtgataaccagttgtatagttttggtactattaaaacaacagtacatcttattatgctttcctaattcagCATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAGCATCGGAATACCGACCCGTGTCCAGACTGCCTTCCGTATGTCAGAAGTT
       | |  || |        | || |  ||| |       |  |  | |      |  ||| |    |||   |||||||     ||  | |      ||||||| |||||||||| ||||| |||||||||||||| ||  | ||||| || || ||  | || || ||||| |||||||||||| | |||   || |||
tatgcgatatcatgattggatcatatggtacgcttttagatgtgaaattcaca-cacaagcgctaattgttcaatgctacatctggc-gtggatgctgg---cagCATGATGGCCACTGTTATGAACGCTATATTTCTTCAGGCCTCAATGGAAAGTATTGGCGTGCCCACACGTGTGCAGACTGCCTTCAGAATGAATGAGGTT

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|13126431|gb|BG317001.1|BG317001
EST:     TCTTGGGCTGGATGTAGTGGGCTTGACCGCTCATCTGCGGATTACATCGG                         CATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAG
genomic: TCTTGGGCTGGATGTAGTGGGCTTGACCGCTCATCTGCGGATTACATCGGgtaagatgtt ... cctaattcagCATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAG
EST: gi|76285329|gb|DV024897.1|DV024897
EST:     GCGGATTACATCGG                         CATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAG
genomic: GCGGATTACATCGGgtaagatgtt ... cctaattcagCATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAG
EST: gi|60343359|gb|DN210332.1|DN210332
EST:     GATTACATCGG                         CATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAG
genomic: GATTACATCGGgtaagatgtt ... cctaattcagCATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAG
EST: gi|91878695|gb|EB408652.1|EB408652
EST:     GATTACATCGG                         CATGCTGGCCACTGTGATGAATGTTATA-TTCTTCAAGCGACGATGGAGAG
genomic: GATTACATCGGgtaagatgtt ... cctaattcagCATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagttttggtactattaaaacaacagtacatcttattatgctttcctaattcagCATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAGCATCGGAATACCGACCCGTGTCCAGACTGCCTTCCGTATGTCAGAAGTT
                                            tcctaat  putative branch site (score: 2)
                                       tgctttcct  CT-rich tract
          tactattaaaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actctactgttcattctggaaggcattcttgtgataaccagttgtatagttttggtactattaaaacaacagtacatcttattatgctttcctaattcagCATGCTGGCCACTGTGATGAATGCTATATTTCTTCAAGCGACGATGGAGAGCATCGGAATACCGACCCGTGTCCAGACTGCCTTCCGTATGTCAGAAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT