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

gtaagattgggttttccgcagtgaatgcaagtcacatactctgtaattatctttaaagtactgaaaagatttttctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCTGGAATGAGTTTGGCAAATCAATCAAGCTGGGTATCATCGAAGACGCGAC

Basic information

species Zea mays
transcript GRMZM2G141931_T01
intron # 11
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 11
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 11
gtaagattgggttttccgcagtgaatgcaagtcacatactctgtaattatctttaaagtactgaaaagatttttctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCTGGAATGAGTTTGGCAAATCAATCAAGCTGGGTATCATCGAAGACGCGAC
     |    ||| || |  |  |   || |||| ||||| | || ||||  |  || |     | |   | |||| || ||||||||||| ||||| |  ||||||||||| ||||||||||| ||||||||||||||||||||||| |||||| ||||| |||| ||||| |||||||| ||
---gtaacaagttctctgtgg--atcacaggtcatatactgt-tatttatgatgtaattctcacataa--tcttctgtactcagATGAAGAAAAAAGTGCAATGGAGGAGAAAAAGGGCCAGTATGCCAAGTTCTGGAATGAGTTTGGAAAATCAGTCAAGTTGGGCATCATTGAAGACGCAAC

upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA14G40320.3 (Glycine max), 3'ss of exon 11
-------------------------------------------------------------------------gtaagattgggttttccgcagtgaa----tgcaa---gtcacatactctgtaattatctttaaagtactgaaaagatttttctctaat-cagATGAAGAGAAAAG--------CGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCTGGAATGAGTTTGGCAAATCAATCAAGCTGGGTATCATCGAAGACGCGAC---
                                                                         ||   |||| |||| |     |  |    | |||   || |  |  |   | | |    || |   |||    |  |   |||  |||   |||| | |||| |          || |  || |||||||| || || ||  | |||||||||||||||||||| ||||| || || || ||||||||||| || || ||   
gtatggtttaatagttatgagtttcatctgttggaatccctatttttttatgggctaaggttgaccaaaacacgtgtaattgtgtttgctttgttataccatttcaaaatgtaaggtgtttcttgaattctgttcattgactttgtacttccatcttaaatattgatgcacagaagATGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCTGGAATGAGTTTGGTAAATCCATTAAACTTGGTATCATCGAGGATGCCACCAA

upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 11
--------------------------------------------------------------------------------------------------------------gtaagattgggttttccgcagtg---aatgcaagtcacatactctgta-attatctttaaagtactgaaaagatttttctctaat---cagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCTGGAATGAGTTTGGCAAATCAATCAAGCTGGGTATCATCGAAGACGCGAC
                                                                                                               |  |       ||| |  | ||    | ||   ||  | | |||||  |||  ||||  | | |    || |||      | ||   |||| ||   |  |   || |   | |||||||| || || ||  |||||||||||||||||||||| ||||| || || || ||||||||||| || || | 
ggtatggtgtaataattatgagtttcatctgttggaatccctatttttttatgggctaaggtttaccagaactcgtgtatcagtctagaatacttgtcttgttgtgtttgctttgtcataccttttcataatgtaagaggcgtttcttaaattctgttcattgactttgtacttccatcaatattaaatattgatgcacaGAAGATACGTCATCTGACAATAATGAGAAGAAAGGTCAATATTCCAAGTTCTGGAATGAGTTTGGTAAATCCATTAAACTTGGTATCATCGAGGATGCCA-

upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 11
-------------------------------------------------------------------------gtaagattgggttttccgcagtgaa----tgcaa---gtcacatactctgtaattatctttaaagtactgaaaagatttttctctaat-cagATGAAGAGAAAAG--------CGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCTGGAATGAGTTTGGCAAATCAATCAAGCTGGGTATCATCGAAGACGCGAC
                                                                         ||   |||| |||| |     |  |    | |||   || |  |  |   | | |    || |   |||    |  |   |||  |||   |||| | |||| |          || |  || |||||||| || || ||  | |||||||||||||||||||| ||||| || || || ||||||||||| || || ||
gtatggtttaatagttatgagtttcatctgttggaatccctatttttttatgggctaaggttgaccaaaacacgtgtaattgtgtttgctttgttataccatttcaaaatgtaaggtgtttcttgaattctgttcattgactttgtacttccatcttaaatattgatgcacagAAGATGCATCCTCTGACAATGATGAGAAGAAAGGTCAATATTCTAAGTTCTGGAATGAGTTTGGTAAATCCATTAAACTTGGTATCATCGAGGATGCCAC

upper sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 11
------------------------------------------------------------------------------------gtaagattgggttttccgcagtgaatgcaagtcaca-----tactctgtaattatctttaaagtactgaa-aagatttttctctaat------cagATGAAGAGAAA---AGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCTGGAATGAGTTTGGCAAATCAATCAAGCTGGGTATCATCGAAGACGCGAC
                                                                                      |    ||  | |   ||| || || | ||| ||      | |||| | |||    ||    |  | |   |  ||    || |||      ||||||  || ||    || ||    || |||||||| || ||||| || ||||||||||||||||||||||| || || || || ||||| || ||||| ||   
gtatggtgtcgttaatgtcacaatcttgttctaacttccagaaaatatttttctcccagaagcaatttgcttttaaattttaattgattgctgcctatcttgcaatggattctagtaactgttgctgctctctcatttctcttgccatctttattgatgttgagttccaatatattgcagATGTTGAAAAGTCCAGTGATGATGATGAGAAGAAAGGTCAGTATGCAAAGTTCTGGAATGAGTTTGGCAAGTCCATAAAACTTGGTATTATTGAAGATGC---

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:     GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAG                         ATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
genomic: GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgg ... ctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
EST: gi|211354989|gb|FL245114.1|FL245114
EST:     GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAG                         ATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
genomic: GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgg ... ctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
EST: gi|211114829|gb|FL096555.1|FL096555
EST:     CTGATGAGTACAGCAACAAGGATAAGACAG                         ATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
genomic: CTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgg ... ctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
EST: gi|30306589|gb|CD001262.1|CD001262
EST:     GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAG                         ATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
genomic: GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgg ... ctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
EST: gi|31354312|gb|CD438669.1|CD438669
EST:     GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAG                         ATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
genomic: GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgg ... ctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
EST: gi|67017884|gb|CO446633.1|CO446633
EST:     GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAG                         ATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
genomic: GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgg ... ctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
EST: gi|50339539|gb|CO534665.1|CO534665
EST:     GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAG                         ATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
genomic: GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgg ... ctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
EST: gi|60344141|gb|DN211114.1|DN211114
EST:     GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAG                         ATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
genomic: GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgg ... ctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
EST: gi|31356123|gb|CD440480.1|CD440480
EST:     GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAG                         ATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
genomic: GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgg ... ctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
EST: gi|20208078|gb|BQ134167.1|BQ134167
EST:     GAAACTTGTTGAAGAATACTCTGATGAGTACAGCAACAAGGATAAGACAG                         ATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
genomic: GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgg ... ctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
EST: gi|26456287|gb|CA827870.1|CA827870
EST:     GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAG                         ATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
genomic: GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgg ... ctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
EST: gi|67024193|gb|CO452942.1|CO452942
EST:     GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAG                         ATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
genomic: GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgg ... ctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
EST: gi|7227450|gb|AW566091.1|AW566091
EST:     GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAG                         ATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
genomic: GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgg ... ctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
EST: gi|21987561|gb|BQ779089.1|BQ779089
EST:     GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAG                         ATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
genomic: GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgg ... ctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
EST: gi|67040100|gb|CO466355.1|CO466355
EST:     GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAG                         ATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT
genomic: GAAACTTGCTGAAGAAGACCCTGATGAGTACAGCAACAAGGATAAGACAGgtaagattgg ... ctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcacatactctgtaattatctttaaagtactgaaaagatttttctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCTGGAATGAGTTTGGCAAATCAATCAAGCTGGGTATCATCGAAGACGCGAC
                                        tttttctct  CT-rich tract
              taattatctttaaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattgggttttccgcagtgaatgcaagtcacatactctgtaattatctttaaagtactgaaaagatttttctctaatcagATGAAGAGAAAAGCGAGATGGAGGAGAAGAAGGGCCAGTACGCCAAGTTCTGGAATGAGTTTGGCAAATCAATCAAGCTGGGTATCATCGAAGACGCGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA