Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttatgctgctggtggtttatccacttccattatagtgtctgagatctggaatacagcttgtgggaagtaacgctgtcgcttgatttttttgtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAAGAAGTTCCAGAACGTGTCCAAGGAGGGACTGAAGC

Basic information

species Zea mays
transcript GRMZM2G141931_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 13
gtattttatgctgctggtggtttatc-cacttccattatagtgtctgagatctggaatacagcttgtgggaagtaacgctgtcgcttgatttttttgtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAAGAAGTTCCAGAACGTGTCCAAGGAGGGACTGAAGC
        | ||||      |||||  |  ||  || |     ||  | |     | |   | |    |||  | |  ||    |||   || | | ||  ||||||| |||| |||||| ||||| || ||||||||| ||||||| ||||| |||||||||||||||||||||||||||||||| ||||||||||| || || |
-----gggtactgcaccacatttattgcttttttatgagctcctccaatagaattactctggatccctggagctta-actaatacttttgttatcttttgttgcagGTTATCTACTTCACTGACCCTGTTGACGAGTACTTGATGCAATACCTCATGGACTACGAGGACAAGAAGTTCCAGAACGTCTCCAAGGAGGGTCTCAAAC

upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 13
--------------------------------gtat-tttatgctgctggtggtttatccacttccattatagtgtctgagatctggaatacagcttgtgggaagtaacgctgtcgcttgatttttttg-tttg-tgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAAGAAGTTCCAGAACGTGTCCAAGGAGGGACTGAAGC
                                |||| |||   ||  |  | |||  |  |    ||||    | |||    |   ||     | |  |   | ||         |  |  | ||||   |||| | ||||| || |||||||| || || || || |||||| ||||||| ||||||||||| || || |||||||||||||| || ||||||||||||||  |||| |
gtacaatttaaattgtttgatttttattacaagtatatttgctctattatttgttcttttaaaaacatttgtctttctattctgctgagagatgatgatttaatgtcttctaaatgtattttcttttgaatttgctacagGTTATTTTCTTCACGGATCCAGTTGATGAGTACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAAC

upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 13
------------------------gtattttatgctgctggtggtttatccacttccattat-agtgtctgagatctg--gaatacagcttgtgggaagtaacgctgtcgcttgatttttttg--tttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAAGAAGTTCCAGAACGTGTCCAAGGAGGGACTGAAGC
                         |||| | |||| ||  |  ||| | | ||   |  || ||  | |    ||||  ||     | |  |   | ||        ||  |  | ||||    ||  | ||||| || |||||||| || || || || || ||| ||||||| ||||||||||| || || |||||||||||||| || ||||||||||||||  ||||  
ggtgcaatttaaattgtttgatttttattatttgct-ctattattttgttctctaaaaacattagcctttctattctgctgaggggtgatgatttaatgtcttctaagcgtattttcttttcaatttcctacaGGTTATTTTCTTCACGGATCCAGTTGATGAATACTTGATGCAATACCTGATGGATTATGAAGACAAGAAGTTCCAAAATGTGTCCAAGGAGGGTTTGAAA-

upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 13
lower sequence: AT4G24190.1 (Arabidopsis thaliana), 3'ss of exon 13
gtattttatgctgctggtggtttatccacttccattatagtgtctgagatctggaatacagcttgtgggaagtaacgctgtcgcttgatttttttgtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAAGAAGTTCCAGAACGTGTCCAAGGAGGGACTGAAGC
               | | |  | | |||    || ||  |   | | |  ||   | || || |       |||| |  || | |       |||| |   ||||||||||||||||| ||||| || || || ||| ||||||| ||||||||||| ||||| ||||| ||||||||||| ||||||||||| ||||||||| 
---------------gtttgcat-tgcacacgaataattcttctttaaa--tgatctccaactcgca-----taacacgttctcata-----cttgtgttcccagGTCATCTTCTTCACAGACCCAGTTGATGAATACTTGATGCAATACCTGATGGATTACGAAGACAAAAAGTTCCAGAATGTGTCCAAGGAAGGACTGAAGG

upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 13
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 13
-------------------------gtattttatgctgctggtggtttatccacttccattatagtgtctgagatctggaatacagcttgtgggaagtaacgctgtcgcttgatttttttgtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAAGAAGTTCCAGAACGTGTCCAAGGAGGGACTGAAGC
                         |  ||| |  | |    || ||  ||   |   ||| |  |  || || |          | || |   || |     | |  ||  ||  || | ||   |||||| || ||||| || ||||| ||||| |||||||||||||| |||||||||||||| || ||||| || |||||||| ||||| ||||| || ||||| |
gtatgattggaaaagataactacttgcttttca-accgtccttgattagtctggtcttattctttt-cctaaggtactatccttggtttttaacaacttgttttctttctgaatcattctatt---gcagGTTATTTTCTTTACTGACCCAGTGGATGAGTACCTGATGCAATACCTGATGGACTATGAAGACAAAAAATTCCAGAATGTGTCAAAGGAAGGCCTGAAAC

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|60348795|gb|DN215768.1|DN215768
EST:     AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAG                         GTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
genomic: AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAGgtattttatg ... gtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
EST: gi|7216906|gb|AW563028.1|AW563028
EST:     AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAG                         GTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
genomic: AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAGgtattttatg ... gtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
EST: gi|211114829|gb|FL096555.1|FL096555
EST:     AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAG                         GTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
genomic: AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAGgtattttatg ... gtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
EST: gi|32839095|gb|CD978776.1|CD978776
EST:     AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAG                         GTCATCTTCTTCACCGACCCCGTGGACGAGT
genomic: AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAGgtattttatg ... gtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGT
EST: gi|14883462|gb|BI273359.1|BI273359
EST:     AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAG                         GTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTTATG
genomic: AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAGgtattttatg ... gtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
EST: gi|67040044|gb|CO466299.1|CO466299
EST:     AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAG                         GTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
genomic: AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAGgtattttatg ... gtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
EST: gi|31354312|gb|CD438669.1|CD438669
EST:     AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAG                         GTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
genomic: AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAGgtattttatg ... gtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
EST: gi|67017884|gb|CO446633.1|CO446633
EST:     AGCTGGAGAAGTCTNCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAG                         GTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
genomic: AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAGgtattttatg ... gtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
EST: gi|50339539|gb|CO534665.1|CO534665
EST:     AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAG                         GTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
genomic: AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAGgtattttatg ... gtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
EST: gi|211114828|gb|FL096554.1|FL096554
EST:     AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAG                         GTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
genomic: AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAGgtattttatg ... gtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
EST: gi|31356123|gb|CD440480.1|CD440480
EST:     AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAG                         GTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
genomic: AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAGgtattttatg ... gtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
EST: gi|20208078|gb|BQ134167.1|BQ134167
EST:     AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAG                         GTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
genomic: AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAGgtattttatg ... gtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
EST: gi|26456287|gb|CA827870.1|CA827870
EST:     AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAG                         GTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGT
genomic: AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAGgtattttatg ... gtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGT
EST: gi|67024193|gb|CO452942.1|CO452942
EST:     AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAG                         GTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG
genomic: AGCTGGAGAAGTCTCCATTCCTCGAGAGGCTAACCAAGAAGAACTACGAGgtattttatg ... gtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggaatacagcttgtgggaagtaacgctgtcgcttgatttttttgtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAAGAAGTTCCAGAACGTGTCCAAGGAGGGACTGAAGC
                                      tttttttgttt  CT-rich tract
                                  ttgatttttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttatgctgctggtggtttatccacttccattatagtgtctgagatctggaatacagcttgtgggaagtaacgctgtcgcttgatttttttgtttgtgcagGTCATCTTCTTCACCGACCCCGTGGACGAGTACCTGATGCAGTACCTGATGGACTACGAGGACAAGAAGTTCCAGAACGTGTCCAAGGAGGGACTGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC