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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcataatgcaatctctattttaagccctgttgcgtcgctcattaactatcagggcctgcgatggtagtaatttggggtaatatatttccactgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACAAGTGGATCAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC

Basic information

species Zea mays
transcript GRMZM2G037923_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 14
-----------------------------------------------------------gtcata-atgcaatctctat---tttaagccctgttgcgtcgctcattaactatcagggcctgcgatggtagtaatttggggtaatatatttccactgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACAAGTGGATCAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC
                                                            | ||  ||    |   |||    |||| |  | |   |   | ||| |  || |  ||| |    | ||  | |  |   ||   |||| |||| |  ||||||||| |||||| ||||||| |||||||||||||| ||||| ||||| | ||||||||||||||| |||||||||||||| || ||||||||||| |||||
gtctgggatgtgtttcttattagtcattttatatcccgaccattcttctttgacgatgaattatccatatgtttcatatggacttaatcattttgttgctccccatgagttaacctggctta--gttgtgatcacctatagtttgatatgtccattattgcagGAACACCTTACTCCCAACAGTCATACAAGGTTAGTGAGTCATTCCCCTTCAAGTGGATCAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGC

upper sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 14
gtcataatgcaatctctattttaagccctgt--tgcgtcgctcattaactat----cagggcctgcga--tggtagtaatttggggtaatatatttccactgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACAAGTGGATCAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC
       |    |  ||  |||||   ||||  ||    |  ||| |||| |    |||    |  ||  |  || | || |   ||   |    |  |||  |  ||||||||||||||| || || || ||||| || || || || || |||| ||| ||||| || ||||||||||||||||| |||||||| || || ||| |
-------tattttagctcgtttaacttctgtgatgaaaggaacatcaactgttcttcagaatttatgactttatatttatctcatgtttgaatcctttact-ttatagGAACTCCTTACACGCAGCAGTCCTACAAAGTGAGTGAATCATTTCCTTTCAAATGGATAAACAAGAAGTGGAAAGAAGGATTCCATGTTACCTCAATGAC

upper sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 14
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 14
gtcataatgcaatctctattttaagccctgttgcgtcgctcattaactatcagggcctgcgatggtagtaatttggggtaatatatttc---cactgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACAAGTGGATCAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC
|||   |  ||      ||  ||| |  ||        || ||| | |   |  ||     |||  ||   |||    || |  | |||    | |||   |||||||||||| ||||| ||||| ||||| || ||||| || || || | ||||||||| ||||| |||||||||||||| || ||||| ||||||||| |
gtcggtagtcacgtctcatgataa-ctttgccaatgaacttattgattcataaagc-----atgaaagccgttttacttattccacttcatgtaatgcgatagGAACTCCTTATACCCAGCAATCTTACAAAGTCAGCGACTCATTTCCATTCAAGTGGATAAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGAC

upper sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 14
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 14
--------gtcataatgcaatctctattttaagccctgttgcgtcgctcattaactatcagggcctgcgatggtagtaatttggggtaatatatttccactgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACAAGTGGATCAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC
         ||  |||   |||      || |  | |||   || ||  |||     |  | |   ||    ||  | || ||| ||  | | |||    |     |||||||||||| ||||| || |||||||| || || || || || || |  || ||||| |||||||||||||||||||| |||||||| ||||| ||| |
tcagtctcatccaaatttgatcatggaatttaatcttgtcatgttgcatattgt---tttgagttggcccatgtgtttatatggtgttttctgtttatgtt-----agGAACTCCTTATACCCAGCAGTCATACAAAGTGAGTGAATCCTTTCCCTTTAAATGGATTAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGAC

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|21760105|gb|BQ635646.1|BQ635646
EST:     AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTCTTCCTTAC
genomic: AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGT-TCCCTTAC
EST: gi|78023792|gb|DV492179.1|DV492179
EST:     CATGTCCAAAG                         GAACTCTTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTTCCTTACA
genomic: CATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACA
EST: gi|32869986|gb|CF009668.1|CF009668
EST:     AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTC
genomic: AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTC
EST: gi|21432270|gb|BQ547760.1|BQ547760
EST:     GTCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTTCATTG                         GAACTCTCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTTCCTTAC
genomic: G-CAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTC-CTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTAC
EST: gi|22473314|gb|BU037794.1|BU037794
EST:     AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTTCCTTACA
genomic: AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACA
EST: gi|33097651|gb|CF057611.1|CF057611
EST:     AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTTCCTTACA
genomic: AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACA
EST: gi|33096688|gb|CF056682.1|CF056682
EST:     AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTTCCTTACA
genomic: AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACA
EST: gi|22713641|gb|BU197414.1|BU197414
EST:     AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTTCCTTACA
genomic: AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACA
EST: gi|22545509|gb|BU097868.1|BU097868
EST:     AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTTCCTTACA
genomic: AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACA
EST: gi|24770058|gb|CA405187.1|CA405187
EST:     GAGCTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTTCCTTACA
genomic: GAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACA
EST: gi|31355521|gb|CD439878.1|CD439878
EST:     AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTTCCTTACA
genomic: AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACA
EST: gi|21987385|gb|BQ778913.1|BQ778913
EST:     AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTTCCTTACA
genomic: AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACA
EST: gi|87156443|gb|DY401232.1|DY401232
EST:     AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTTCCTTACA
genomic: AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACA
EST: gi|78083128|gb|DV511521.1|DV511521
EST:     AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACA
genomic: AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACA
EST: gi|26559413|gb|CA831648.1|CA831648
EST:     AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTTCCTTACA
genomic: AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACA
EST: gi|31356845|gb|CD441202.1|CD441202
EST:     AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAG                         GAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTTCCTTACA
genomic: AGCAATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACA
EST: gi|31350536|gb|CD434893.1|CD434893
EST:     AATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCCTTTCCAAAG                         GAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTTCCTTACA
genomic: AATTGCTGGATCATCCAACGGGAGCTCATTGGTTGTCATGTCCAAAGgtcttgattt ... actgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatcagggcctgcgatggtagtaatttggggtaatatatttccactgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACAAGTGGATCAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC
 cattaac  putative branch site (score: 2)
                                        tttccact  putative PPT
                                 taatatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcataatgcaatctctattttaagccctgttgcgtcgctcattaactatcagggcctgcgatggtagtaatttggggtaatatatttccactgctgcagGAACTCCTTACACCCAACAATCATACAAGGTTAGCGAGTCGTTCCCTTACAAGTGGATCAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG