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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatctgttgcttttttcctttataatacaaatccgccttcacttcaattcttactgtactagctcgatctgcataccattttctatttgccatg...

Basic information

species Zea mays
transcript GRMZM2G162672_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162672_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os05g28200.2 (Oryza sativa), 5'ss of exon 11
TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaagg-catctgttgc--ttttttcctttataatacaaat-ccgccttcacttcaat-tcttactgtactagctcgatctgcataccattttctatttgccatg
||||| || ||||||||||| |||||||||||||| ||||| ||||| ||||| ||||| || ||||||||||| |||||||| || | |||   ||    || | |   || |  | ||||      |||||   |  | ||||  | |  | | |  || ||       || || | |||     
TCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAGgtaaagacatgcattttcattatgttgcttttgtttcaaacattatcttcaaggctgtatcttggtttcattgatt-atgtggtccatgttgtcaacttgt----

upper sequence: GRMZM2G162672_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA16G19390.1 (Glycine max), 5'ss of exon 4
TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatctgttgcttttttcctttataatacaaatccgccttcacttcaattcttactgtactagctcgat-ctgcataccattttctatttgccatg----------
|| ||||| |||||||||||    ||||||||||| ||||| |||||||| || ||||| || || ||||||||||| || || ||            |||  ||| | | |||| | |       | |||  |  |   |    |  || | ||  ||    ||||| ||   ||   |||           
TCTCTTCCAGTTGCTTTTGGTGCTGAAACTGCAAAGTGGATATGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCTGgtaaa----------ttttgatccctca-aatatatacaaataattactatatatacaaacaaaacagttagaaacttttcaccatatttacttaatcattatccttgtcc

upper sequence: GRMZM2G162672_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA18G43310.1 (Glycine max), 5'ss of exon 12
-TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatctgttgcttttttcctttataatacaaatccgccttcacttcaattcttactgtactagctcgatctgcataccatttt--ctatttgccatg
 || ||||| |||||||||||    ||||||||||| ||||| |||||||| || ||||| || || ||||||||||| || || ||    | |||| | ||     | ||||  | | |   ||  |   | |||     || ||   |      ||  ||||     ||    |||  || ||
GTCTCTTCCAGTTGCTTTTGGTGCTGAAACTGCAAAGTGGATCTGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCGggtaaat--tttgttcccttaaatatatata-caaataattgctctatatacaaacaaaacagttagaaacttgtcaccatattcacttaatcattatccttg

upper sequence: GRMZM2G162672_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA07G18470.1 (Glycine max), 5'ss of exon 12
TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatctgttgcttttttcctttataatacaaatccgccttcacttcaattcttactgtactagctcgatctgcataccatttt--ctatttgccatg---
|| ||||| |||||||||||    ||||||||||| ||||| |||||||| || ||||| || || ||||||||||| || || ||      | |      |    | ||||  |  |||    ||  | | |||     || ||   |     |||  ||||     ||    |||  || ||   
TCTCTTCCAGTTGCTTTTGGTTCTGAAACTGCAAAGTGGATATGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCTGgtaaa----ttttgatccctcaaatatatacaaataattactctata-tacaaacaaaacagttagaaacttatcaccatatttacttaatcattatccttgtcc

upper sequence: GRMZM2G162672_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv08s0105g00590.t01 (Vitis vinifera), 5'ss of exon 12
TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatctgttgcttttttcctttataatacaaatccgccttcacttcaattcttactgtactagctcgatctgcataccattttctatttgccatg---
|| || || || || |||||    |||||||| |||||||||||||| || || ||||| |||||||| ||||| || || || |    || | ||||| || |   || |  |     |    |||   || |||  || |   | ||  ||    |||  |||  | |  | |    |     
TCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGTGTGGGTGCTATTGACATCACTCAGTTATCAGTGGCTGgtatataatat-ttgctgttgttggtttttttttttttttttcttt-ttttaatgtttgcatcaata-ttcatgttgctgacccctataaaatgaagacttct

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|211036110|gb|FL230102.1|FL230102
EST:     AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG                         GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
genomic: AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatc ... atctcttcagGTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
EST: gi|71759623|gb|DR957560.1|DR957560
EST:     AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG                         GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
genomic: AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatc ... atctcttcagGTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
EST: gi|32940940|gb|CF045759.1|CF045759
EST:     AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGTAG                         GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
genomic: AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatc ... atctcttcagGTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
EST: gi|211036106|gb|FL230098.1|FL230098
EST:     AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG                         GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
genomic: AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatc ... atctcttcagGTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
EST: gi|71314948|gb|DR794088.1|DR794088
EST:     AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG                         GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
genomic: AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatc ... atctcttcagGTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
EST: gi|211036107|gb|FL230099.1|FL230099
EST:     AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG                         GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
genomic: AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatc ... atctcttcagGTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
EST: gi|78120047|gb|DV538431.1|DV538431
EST:     AAATGGATTTGTGTTGGAGCAATTGATATCACTTCA-TTATCTGTTGCAG                         GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTG
genomic: AAATGGATTTGTGTTGGAGCAATTGATATCACT-CAATTATCTGTTGCAGgcaaggcatc ... atctcttcagGTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTG
EST: gi|71324982|gb|DR799184.1|DR799184
EST:     AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG                         GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
genomic: AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatc ... atctcttcagGTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
EST: gi|149110076|gb|EE293890.2|EE293890
EST:     AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG                         GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
genomic: AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatc ... atctcttcagGTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
EST: gi|71426127|gb|DR807177.1|DR807177
EST:     AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG                         GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
genomic: AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatc ... atctcttcagGTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
EST: gi|71763867|gb|DR961804.1|DR961804
EST:     AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG                         GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
genomic: AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatc ... atctcttcagGTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
EST: gi|32931186|gb|CF035998.1|CF035998
EST:     AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG                         GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
genomic: AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatc ... atctcttcagGTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
EST: gi|32940989|gb|CF045808.1|CF045808
EST:     AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG                         GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
genomic: AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatc ... atctcttcagGTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
EST: gi|148929759|gb|EE285358.2|EE285358
EST:     AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATTTGTTGCAG                         GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC
genomic: AAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatc ... atctcttcagGTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAGgcaaggcatctgttgcttttttcctttataatacaaatccgccttcacttcaattcttactgtactagctcgatctgcataccattttctatttgccatg

- - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - GGAGCA