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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCATCGCTATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgacttaacatagtacctccattgttgaaatggttttgcatgctgtttttgttatctctaagttgtatttgaactttgatgctatctaaataggttttcttgtgctatatttccag

Basic information

species Zea mays
transcript GRMZM2G421857_T04
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421857_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 5
ACCATCGCTATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtg-acttaacatagtacctccattgttgaaatggttttgcatgctgtttttgttatctctaagttgtatttgaactttgatgctatctaaataggttttcttgtgctatatttccag--
|| || |||||||| || ||||||||||| ||||| |||||||| |||||||||||||||||||||||||  |||||| | ||| |||||   || |||||||  | | ||   |||    || ||  |  ||   ||    |    || || || |  | | | | ||     || | |   | ||  ||||||    | | ||  |   ||  | |     
ACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGTGGTGTCTCAGTTCCTGCCCTTGACAAAGATGCTTTGTGGCATTTTAAGCCAGAAAAACTAGgtaaagtattttgtata----cttcaggggggaggggggggggttaccttttgttatcctttttcattta-gcatgcagtgcaaggcactctaaaatcatctcctattatcattatgctgcag

upper sequence: GRMZM2G421857_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 5
ACCATCGCTATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgacttaacatagtacctccattgttgaaatggttttgcatgctgtttttgttatctctaagttgtatttgaactttgatgctatctaaataggttttcttgtgctatatttccag
|| || ||||  |  || || ||||| ||||||||||||||||| || ||||| || || |||||||||  | | ||||||||||| || | |||  | ||||       ||  || |       ||  ||  |  ||| |  ||      || ||  |   |      | |||    | ||||  | | |    |  ||   | |||  |         
ACTATTGCTAAAAGATCTGGTGATGTCTATATTCCTCGTGGTGTCTCTGTTCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgtaccagacaaat-tatttttctttttactgttaaagttctatatagaaaattagtattacgtggaccattttt---ttctgatattctatg---atattcattggtgacag--------

upper sequence: GRMZM2G421857_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 5
ACCATCGCTATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgacttaacatagtacctccattgttgaaatggttttgcatgctgtttttgttatctctaagttgtatttgaactttgatgctatctaaata-ggttttcttgtgctatatttccag
|| || ||||     || || ||||| ||||||||||||||||| || ||||| || || |||||||||  | | ||||||||||| || | |||  | ||||    |   ||| | ||  |   || ||        | |  | | | | |||   |  |  ||||  ||  || ||  |  | |    || ||  | ||  || |||  |         
ACTATTGCTAAACGATCTGGTGATGTCTATATTCCTCGTGGTGTCTCTGTTCCAGCACTCGACAAAGATACACTTTGGGAATTTCAACCTAAGAAAATTGgta----ccagacaaattatttttcttttta------ctgttaaagttttatttagaaaat--aagtattacgtggaccatttttcctgatatatgtgattcactggtgacag--------

upper sequence: GRMZM2G421857_T04 (Zea mays), 5'ss of exon 6
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 5
ACCATCGCTATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagt-gacttaacatagtacctccattgtt--gaaatggttttgcatg-ctgtttttgttatctctaagttgtatttgaactttgatgctatctaaataggttttcttgtgctatatttccag
||||| || |  |  || || ||||| || |||||||||||||| || |||||||| |||||||||||| || | |||||||| ||||| |  ||  |||||| |  |   ||  ||  |      |  ||  ||  || |||   |   || || || | || |   | |    ||   ||| ||||   | | |  |   | |  | ||| ||         
ACCATTGCAAAAATATCTGGTGATGTCTACATTCCTCGTGGTGTATCTGTTCCTGCACTTGACAAAGATATACTCTGGGAATTCCAGCCTAAAAAATTAGgtaatcaaagaaatgtatcattatagtcatttggaggtgatttgaaaaaactattattttgatttgagactc---ttcatactctgat-taaaccagtttcatctcttggtggtag--------

upper sequence: GRMZM2G421857_T04 (Zea mays), 5'ss of exon 6
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 5
ACCATCGCTATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgacttaacatagtacctccattgttgaaatggttttgcatgctgtttttgttatctctaagttgtatttgaactttgatgctatctaaataggttttcttgtgctatatttccag
|| || ||||  |  || || ||||| |||||||||||||||||||| || || |||||||||||||||  | | ||||| || ||||| | ||| ||||||| ||  | || ||  ||   |    ||   | | | ||||    ||||  ||          |  |||||     | |||||||||   |||| | ||| ||    || |   | |||
ACTATTGCTAAGAGATCTGGTGATGTCTATATTCCTCGTGGTGTTTCTGTCCCAGCCCTTGACAAAGATACACTATGGGAGTTCCAGCCCAAGAAACTAGgtactgcttgaatatgctaatac----gtgatagttggtttgtggtctgtcctt----------aactgtat-----cattgatgctaataaaattgctttcctctcactgt---tgcag

upper sequence: GRMZM2G421857_T04 (Zea mays), 5'ss of exon 6
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 5'ss of exon 5
ACCATCGCTATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgacttaacatagtacctccattgttgaaatggttttgcatgctgtttttgttatctctaagttgtatttgaactttgatgctatctaaataggttttcttgt-gctatatttccag
 | || ||  || |||     |||||||||||||||||||| ||| |||| ||||| ||||| | | |      |||||||||  | || |  | ||| |  ||||| ||    |  || |||     |||   |||| |      | || | |||| ||| | ||    |   |    || || || |  | | |  | | ||||| |  ||| ||||  
GCTATTGCACTTCAGTGTCAGGATGTGTATATTCCTCGTGGAGTTGCAGTGCCTGCTCTTGATAGAAAGAGGCAGTGGGAATTCAAACCTA-AAGGCTTG--Agtgagtt----tgctatctc-----ttg---tggtctgttcaccagtatctgttctctttcagcaaaaacag----tttat-ctttacagaaaattgtgcttgttgtcatacttcct-

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|18649012|gb|BM497831.1|BM497831
EST:     TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAG                         GTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
genomic: TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgactt ... atatttccagGTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
EST: gi|32838516|gb|CD978194.1|CD978194
EST:     TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACAAAGCTAG                         GTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
genomic: TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgactt ... atatttccagGTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
EST: gi|32925687|gb|CF030499.1|CF030499
EST:     TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACAAAGCTAG                         GTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
genomic: TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgactt ... atatttccagGTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
EST: gi|32921771|gb|CF026583.1|CF026583
EST:     TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAG                         GTGTTGGAGATGTCATTACAGGTGGAGATCTATACGCT
genomic: TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgactt ... atatttccagGTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
EST: gi|32924704|gb|CF029516.1|CF029516
EST:     TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACAAAGCTAG                         GTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
genomic: TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgactt ... atatttccagGTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
EST: gi|32925234|gb|CF030046.1|CF030046
EST:     TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACAAAGCTAG                         GTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
genomic: TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgactt ... atatttccagGTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
EST: gi|32838453|gb|CD978131.1|CD978131
EST:     TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACAAAGCTAG                         GTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
genomic: TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgactt ... atatttccagGTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
EST: gi|211532167|gb|FL123441.1|FL123441
EST:     TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACAAAGCTAG                         GTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
genomic: TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgactt ... atatttccagGTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
EST: gi|32827480|gb|CD967158.1|CD967158
EST:     TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACAAAGCTAG                         GTGTTGGAGATGTCATCACAGGTGGAGATC
genomic: TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgactt ... atatttccagGTGTTGGAGATGTCATCACAGGTGGAGATC
EST: gi|6636981|gb|AW261253.1|AW261253
EST:     TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAG                         GTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
genomic: TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgactt ... atatttccagGTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
EST: gi|32848240|gb|CD987921.1|CD987921
EST:     TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACAAAGCTAG                         GTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
genomic: TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgactt ... atatttccagGTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
EST: gi|211541195|gb|FL123492.1|FL123492
EST:     TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAG                         GTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
genomic: TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgactt ... atatttccagGTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
EST: gi|32934325|gb|CF039137.1|CF039137
EST:     TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACAAAGCTAG                         GTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT
genomic: TCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgactt ... atatttccagGTGTTGGAGATGTCATCACAGGTGGAGATCTATACGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCATCGCTATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGTATTGTGGGAATTTCAGCCAACGAAGCTAGgtagtgacttaacatagtacctccattgttgaaatggttttgcatgctgtttttgttatctctaagttgtatttgaactttgatgctatctaaataggttttcttgtgctatatttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG