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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgcctaacataaactataaatctccaggtcgaacttgaacttggtgaacttattgttgttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATTGCTCATGGGGTGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATT

Basic information

species Zea mays
transcript GRMZM2G134396_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134396_T03 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os07g49270.1 (Oryza sativa), 3'ss of exon 15
gttagtgccta-acataaactataa-atctccaggtcgaacttgaacttggtgaacttattgttgttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATTGCTCATGGGGTGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATT
||   |||  |  || | | |  |  ||    || |  | |  | |   | || | | ||  || || |||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||| |||||||| ||||| ||  ||||||| |||||||| || ||||| |||||||
gtatatgctaatgcacatatttgagtattcatagatttaccccggaaaagttgcattgatgattcttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATTGCTCACGGGGTTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATT
















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|67028452|gb|CO457201.1|CO457201
EST:     GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
genomic: GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgttagtgcct ... ttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
EST: gi|32837964|gb|CD977642.1|CD977642
EST:     GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
genomic: GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgttagtgcct ... ttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
EST: gi|21987227|gb|BQ778755.1|BQ778755
EST:     GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
genomic: GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgttagtgcct ... ttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
EST: gi|26557914|gb|CA830149.1|CA830149
EST:     GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGCGGGGAG                         GCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
genomic: GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgttagtgcct ... ttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
EST: gi|32832752|gb|CD972430.1|CD972430
EST:     GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
genomic: GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgttagtgcct ... ttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
EST: gi|74237693|gb|DT645607.1|DT645607
EST:     GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
genomic: GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgttagtgcct ... ttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
EST: gi|211424036|gb|FL301688.1|FL301688
EST:     GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
genomic: GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgttagtgcct ... ttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
EST: gi|71299098|gb|DR785546.1|DR785546
EST:     GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
genomic: GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgttagtgcct ... ttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
EST: gi|211424037|gb|FL301689.1|FL301689
EST:     GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
genomic: GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgttagtgcct ... ttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
EST: gi|211424038|gb|FL301690.1|FL301690
EST:     GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
genomic: GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgttagtgcct ... ttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
EST: gi|78121620|gb|DV540004.1|DV540004
EST:     GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
genomic: GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgttagtgcct ... ttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
EST: gi|211424039|gb|FL301691.1|FL301691
EST:     GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGG-AG                         GCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT
genomic: GTGAGTCCAAGGGCATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgttagtgcct ... ttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctataaatctccaggtcgaacttgaacttggtgaacttattgttgttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATTGCTCATGGGGTGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATT
                                             ttatcttc  CT-rich tract
                                 aacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgcctaacataaactataaatctccaggtcgaacttgaacttggtgaacttattgttgttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATTGCTCATGGGGTGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA