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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGCAGGAGCTGGTGCCCGGGTGCAGCAAGGTCACGGGCAAGGCCGGCATGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgacccaccggcaccgtcctgcttcatcttccccgcttctcccagctagccagctagttattccgcgatcgctcaccgccgggtctccttgcgcgcag

Basic information

species Zea mays
transcript GRMZM2G101350_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101350_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g47660.1 (Oryza sativa), 5'ss of exon 3
CCTGCAGGAGCTGGTGCCCGGGTGCAGCAAGGTCACGGGCAAGGCCGGCATGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgac-ccaccgg--caccgtcctgcttcatcttccccgcttctcccagctagccagctagttattccgcgatcg-ctcaccgccgggtctccttgcgcgcag
||||||||||||||||||||| |||| ||||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||   | ||| ||   || |  ||| || |||     | ||| || |   || ||  | |  || |||  |||  | ||  |||   ||   |  | |  ||||
CCTGCAGGAGCTGGTGCCCGGTTGCAACAAGGTCACCGGCAAGGCCGGCATGCTCGACGAGATCATCAACTACGTGCAGTCCCTGCAGAAGCAAGTCGAGgtacgagcaccaacgctccagctccctcctccatggatgcagct-ctgctttcttgctcggtgtttgttcatcgaagggcttgccgt--ggctgctgttcttgcag

upper sequence: GRMZM2G101350_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S68_190V6.1 (Physcomitrella patens), 5'ss of exon 3
CCTGCAGGAGCTGGTGCCCGGGTGCAGCAAGGTCACGGGCAAGGCCGGCATGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgta-----ccgacccaccggcaccgtcctgct--tcatcttccccgcttctcccagctagccagctagttattcc--gcgatcgctcaccgccgggtctccttgcgcgcag------------------------
||||||||| || || ||||| ||| |||| ||||| |||||||| | |||||| ||||||||||||||||| || || ||||| ||    ||||| || |||     |  |||||    || ||  |||||  |  | ||||   | | ||  ||  | ||  || |||||  |  | |||   |    | |  || |      |    |                        
CCTGCAGGACCTCGTACCCGGCTGCCGCAAAGTCACCGGCAAGGCAGTCATGCTTGACGAGATCATCAACTATGTTCAATCCCTCCAACGACAAGTTGAAgtatgtctcttacccattttcaacgcactgctaatgctattccattcatgtcttaggcacccttcttgttatcgctagtgatgaattgtagtctagtattgagttgtatcgtacactttgttatcttttttacag

upper sequence: GRMZM2G101350_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S69_95V6.1 (Physcomitrella patens), 5'ss of exon 2
CCTGCAGGAGCTGGTGCCCGGGTGCAGCAAGGTCACGGGCAAGGCCGGCATGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgaccca--ccggcaccgtcctgcttcatcttccccgcttctcccagctagcca--gctagttattccgcgat----cgctcaccgccgggtctcctt-gcgc-gcag
| ||||||| || || || || ||| |||| ||||| ||||| || | ||||||||| || |||||||| |||||||||||||| ||    |||||||||||||   ||     |  | |||| ||  | ||   |    | |  |   ||  | |    |  | | ||  |  | |     | | ||  ||   | |  || | |  ||||
CTTGCAGGACCTTGTTCCTGGCTGCCGCAAAGTCACTGGCAAAGCAGTCATGCTCGATGAAATCATCAATTACGTCCAGTCCCTCCAACGTCAAGTCGAGgtacatccctcattctccgccgttcta-tacacaattgaaggtggtgatagggatctgctgtaattcatatcaggttatgatgttaacttccacattttttttgtgttgcag

upper sequence: GRMZM2G101350_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S226_51V6.1 (Physcomitrella patens), 5'ss of exon 2
CCTGCAGGAGCTGGTGCCCGGGTGCAGCAAGGTCACGGGCAAGGCCGGCATGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtac------cgacccaccggcaccgtcctgcttcatcttccccgcttctcccag-ctagccagctagt-tattccgcgatcgctcaccgc--cgggtctccttgcgcgcag---------------------------------------------------------------
| ||||||| || || || |||||||  || || |||||||| || | |||||||||||||||||||||||| || || | ||| |||   |||||||| ||||      |  | | |   | |  ||  | | | || | ||  |   | |  | |||||  |  ||| |||   |   |   |||   |  ||||         |   ||                                                               
CTTGCAGGACCTCGTTCCTGGGTGCAAGAAAGTTACGGGCAAAGCGGTCATGCTCGACGAGATCATCAACTATGTTCAATTCCTCCAGCGCCAAGTCGAAgtacgtctagcctctctctctctctctctcgttccttccttccttccaattcaggtctagcgtgggagtatatctaggagtaaatcagaacttcgggatgttccatgtcaagctttgatatgcccccaatttgtttcgcagcatctatcaatgaggctggcatccgtgtgctcag

upper sequence: GRMZM2G101350_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S226_51V6.2 (Physcomitrella patens), 5'ss of exon 2
CCTGCAGGAGCTGGTGCCCGGGTGCAGCAAGGTCACGGGCAAGGCCGGCATGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtac------cgacccaccggcaccgtcctgcttcatcttccccgcttctcccag-ctagccagctagt-tattccgcgatcgctcaccgc--cgggtctccttgcgcgcag-----------------------------
| ||||||| || || || |||||||  || || |||||||| || | |||||||||||||||||||||||| || || | ||| |||   |||||||| ||||      |  | | |   | |  ||  | | | || | ||  |   | |  | |||||  |  ||| |||   |   |   |||   |  ||||         |   ||                             
CTTGCAGGACCTCGTTCCTGGGTGCAAGAAAGTTACGGGCAAAGCGGTCATGCTCGACGAGATCATCAACTATGTTCAATTCCTCCAGCGCCAAGTCGAAgtacgtctagcctctctctctctctctctcgttccttccttccttccaattcaggtctagcgtgggagtatatctaggagtaaatcagaacttcgggatgttccatgtcaagctttgatatgcccccaatttgtttcgcag

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|71446020|gb|DR827070.1|DR827070
EST:     TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAG                         TTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
genomic: TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgaccc ... ttgcgcgcagTTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
EST: gi|78080061|gb|DV508473.1|DV508473
EST:     TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAG                         TTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTTGACATC
genomic: TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgaccc ... ttgcgcgcagTTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
EST: gi|78090318|gb|DV518692.1|DV518692
EST:     TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAG                         TTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
genomic: TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgaccc ... ttgcgcgcagTTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
EST: gi|60338634|gb|DN205607.1|DN205607
EST:     TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAG                         TTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
genomic: TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgaccc ... ttgcgcgcagTTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
EST: gi|50335489|gb|CO530615.1|CO530615
EST:     TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAG                         TTTTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
genomic: TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgaccc ... ttgcgcgcagTTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
EST: gi|78120916|gb|DV539300.1|DV539300
EST:     TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAG                         TTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
genomic: TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgaccc ... ttgcgcgcagTTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
EST: gi|76293816|gb|DV033384.1|DV033384
EST:     TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAG                         TTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
genomic: TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgaccc ... ttgcgcgcagTTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
EST: gi|71768486|gb|DR966423.1|DR966423
EST:     TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAG                         TTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
genomic: TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgaccc ... ttgcgcgcagTTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
EST: gi|76293282|gb|DV032850.1|DV032850
EST:     TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAG                         TTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
genomic: TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgaccc ... ttgcgcgcagTTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
EST: gi|71312226|gb|DR792635.1|DR792635
EST:     TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAG                         TTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC
genomic: TGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgaccc ... ttgcgcgcagTTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 3 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 17

CCTGCAGGAGCTGGTGCCCGGGTGCAGCAAGGTCACGGGCAAGGCCGGCATGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgaccc ... ttgcgcgcagTTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATCGTCGAGGACCTCTTCGGCCGCCAGCTGAAGCAGGCGTGCGGCCCGGCGG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 11

CCTGCAGGAGCTGGTGCCCGGGTGCAGCAAGGTCACGGGCAAGGCCGGCATGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgaccc ... ttgcgcgcagTTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATCGTCGAGGACCTCTTCGGCCGCCAGCTGAAGCAGGCGTGCGGCCCGGCGG


Block sizes: 22 (upstream exon), 31 (downstream exon)
Score: 3

CCTGCAGGAGCTGGTGCCCGGGTGCAGCAAGGTCACGGGCAAGGCCGGCATGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgaccc ... ttgcgcgcagTTCTTGTCCATGAAGATCGCCGCTTCCAACCCGGTGGTGAGCTTCGACATCGTCGAGGACCTCTTCGGCCGCCAGCTGAAGCAGGCGTGCGGCCCGGCGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGCAGGAGCTGGTGCCCGGGTGCAGCAAGGTCACGGGCAAGGCCGGCATGCTCGACGAGATCATCAACTACGTCCAGTCCCTGCAGAAGCAAGTCGAGgtaccgacccaccggcaccgtcctgcttcatcttccccgcttctcccagctagccagctagttattccgcgatcgctcaccgccgggtctccttgcgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG