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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcaaaccctccgtccctcccatcgatcctccgaccagatctcgcgattcccgactcaaactaatatctctgaccccgaattcatgtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGCGGGGCTGAAGGCGGACGCACGCGTGCTCATCAACCGCGCGCGGGTCGAG

Basic information

species Zea mays
transcript GRMZM2G138128_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138128_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g36710.1 (Oryza sativa), 3'ss of exon 1
gtagcaaaccctccgtccctcccatcgatcctccgaccagatctcgcgattcccgactcaaactaatatctctgaccccgaattcatgtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGCGGGGCTGAAGGCGGACGCACGCGTGCTCATCAACCGCGCGCGGGTCGAG
              || ||   || |    | |   |    || |   |  |||   |  | || || || | |     | ||||     | | |||||| ||||||||||||||  ||||||||||||||||||| ||||| ||||||||||| ||||||||||| ||||||||||||||||||||||||||||||
--------------gtacccatcacctcctcgcgacctctctccccatacacccccatagatctcatctcgccggtgggggattcga---ttcgcagGTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGCGGGGCTCAAGGCGGACGCCCGCGTGCTCATCAACCGCGCGCGGGTCGAG

upper sequence: GRMZM2G138128_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G23580.1 (Glycine max), 3'ss of exon 1
-gtagcaaaccctc-cgtccctcccatcgatcctccgaccagatctcgcgattcccgactcaaactaatatctctgaccccgaattcatgtc---tccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGCGGGGCTGAAGGCGGACGCACGCGTGCTCATCAACCGCGCGCGGGTCGAG
  || | ||  ||  |  |   |   |  |  |   ||  | |  |  | |    ||||      | | |||    |||| || ||  ||||   | | |||||| ||| | ||||| | |   ||||||  |||||| || ||||| ||||||||||||||||| ||||||||||||||||| ||| | || || || |||
gctaacgaatactaacaactaacatttgcaatcaaagaagaaaaataacaaaaaacgacgtcgtttcaaatcg--aaccctgattttgtgtcgttttcgcagGTCGGTGAGGAAGATAGTGAATCTGGACGACCACATTGCGCTGGCCTGCGCGGGGCTGAAGGCCGACGCACGCGTGCTCATAAACAGGGCACGTGTGGAG

upper sequence: GRMZM2G138128_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G05190.1 (Glycine max), 3'ss of exon 1
--------gtagcaaaccctccgtccctcccatcgatcctccgaccagatctcgcgattcccgactcaaactaatatctctgaccccgaattcatgtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGCGGGGCTGAAGGCGGACGCACGCGTGCTCATCAACCGCGCGCGGGTCGAG
         |   |   |  |||| ||    || | |      |||| |            ||  ||||| |||   | ||||    |  |    || | | |||||| ||| | ||||| | |   ||||||| |||||| || ||||||||||||||||||||||| |||||||| |||||||| ||| | || || || |||
caactcaccttatatctctgccgttcccttaataggtgt--aaaccaaaaaaaaacgacgtcgtttcaaattaaa--cactgatttggtgtgt-cgttttcgcagGTCGGTGAGGAAGATTGTGAATCTGGACAACCACATTGCGCTGGCATGCGCGGGGCTGAAGGCCGACGCACGTGTGCTCATAAACAGGGCACGTGTGGAG

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|19770273|gb|BQ034994.1|BQ034994
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|32914285|gb|CF019097.1|CF019097
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGATTTTTT                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|211308682|gb|FL018774.1|FL018774
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|211304621|gb|FL018741.1|FL018741
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GYCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|71432817|gb|DR813867.1|DR813867
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|211304632|gb|FL018752.1|FL018752
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|211304628|gb|FL018748.1|FL018748
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|211304634|gb|FL018754.1|FL018754
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|211037504|gb|FL188134.1|FL188134
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|211219953|gb|FL188165.1|FL188165
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|149051858|gb|EE155986.2|EE155986
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|211304635|gb|FL018755.1|FL018755
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|211304633|gb|FL018753.1|FL018753
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|148952506|gb|EC898333.2|EC898333
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|67039736|gb|CO465991.1|CO465991
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|91873762|gb|EB403719.1|EB403719
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
EST: gi|211222019|gb|FL188175.1|FL188175
EST:     GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAG                         GTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC
genomic: GTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaacc ... gtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgcgattcccgactcaaactaatatctctgaccccgaattcatgtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGCGGGGCTGAAGGCGGACGCACGCGTGCTCATCAACCGCGCGCGGGTCGAG
                                            tgtctcccc  CT-rich tract
                 aaactaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcaaaccctccgtccctcccatcgatcctccgaccagatctcgcgattcccgactcaaactaatatctctgaccccgaattcatgtctccccagGTCCGTGCGCAAGATCGCGTGCCTGGACACCCACATCGCTCTGGCATGCGCGGGGCTGAAGGCGGACGCACGCGTGCTCATCAACCGCGCGCGGGTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG