Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggagaggaatactttcgttgattgctttttttgttctacctgagatgcactgtctcttgttagcaacacatcaatcatagaggaggttatttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTG

Basic information

species Zea mays
transcript GRMZM2G022876_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022876_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g34950.2 (Oryza sativa), 3'ss of exon 2
-ggagaggaatactttcgttgattgctttttttgttctacctgagatgcactgtctcttgttagcaacacatcaatcatagaggaggttatttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTG
     | |   |||||   |  |||   | | |||| |    |  ||   ||   |  |  |||| |      |   |  ||    | | |||||||||||||||||||| |||| ||||| |||||||| || |||||||||||||| |||||  || ||||||||||||||||||||||||||||||| |
tttcaatgtgcactttttgtctttgtactctatgttttggtggttataatctagattataatagctaggagctatgtactgaacctgat-tttgttcttagGAAAACCGTCTGCGTCAAGAAATAGAAGATCTTGAGAAAGATACAGGATACAAGTTGAGAGTTCTTGCACAAAATTATCCTGATACACCAG
















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|211533933|gb|FL079631.1|FL079631
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACA
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACA
EST: gi|13125853|gb|BG316423.1|BG316423
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|16377665|gb|BI992046.1|BI992046
EST:     TACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: TACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|22819283|gb|BU499373.1|BU499373
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211533938|gb|FL079636.1|FL079636
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211533932|gb|FL079630.1|FL079630
EST:     AGAATTTACTACCGTCCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTG
genomic: AGAATTTACTACCGTC-ATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTG
EST: gi|211536947|gb|FL079648.1|FL079648
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGNCAG                         GAAAACCGTTTGCGCCAAGAGATAGA-GACCTG
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTG
EST: gi|211539949|gb|FL079654.1|FL079654
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGAC-TGGAG
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAG
EST: gi|149071910|gb|EE160296.2|EE160296
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211533931|gb|FL079629.1|FL079629
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211539950|gb|FL079655.1|FL079655
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|21809641|gb|BQ667959.1|BQ667959
EST:     ACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: ACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211533934|gb|FL079632.1|FL079632
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGA
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGA
EST: gi|211533928|gb|FL079626.1|FL079626
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211536951|gb|FL079652.1|FL079652
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAG
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAG
EST: gi|211536937|gb|FL079638.1|FL079638
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCACGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211536944|gb|FL079645.1|FL079645
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|14243662|gb|BG841333.2|BG841333
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211539948|gb|FL079653.1|FL079653
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTAC
EST: gi|211536943|gb|FL079644.1|FL079644
EST:     AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAG                         GAAAACCGTTTGCGCC
genomic: AAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGGCCAGgtaggtccag ... ttgttcttagGAAAACCGTTTGCGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcactgtctcttgttagcaacacatcaatcatagaggaggttatttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTG
                                            tttgttctt  CT-rich tract
                                         ttatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggagaggaatactttcgttgattgctttttttgttctacctgagatgcactgtctcttgttagcaacacatcaatcatagaggaggttatttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTG

- - - - - - - - - tgattgc
- - - - - - - - - - - - - - ttttgtt
- - - - - - - - - - - - - - - - - -ctacctg
- - - - - - - - - - - - - - - - - - - - - agatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacaca