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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgctctcttactcctttggtttcttcacatccttatatgctggctatccctttacctatttgtgcttactaatgatatctcacctattctgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATTACCGAAACTGTTCTGGTGGTTGCTCTTTCAAGAAGATATGGGAAGCGGC

Basic information

species Zea mays
transcript GRMZM2G051262_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051262_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g11070.1 (Oryza sativa), 3'ss of exon 2
gtttgtgctctcttactcctttggtttcttcacatcctt--atatgctggctatccctttacctatttgtgctt---actaatgatatctcacctattct------gctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATTACCGAAACTGTTCTGGTGGTTGCTCTTTCAAGAAGATATGGGAAGCGGC
|||||| || |  || || ||  ||||| |||| |  |   || ||||   ||     ||||   |   | | |   ||||||  ||| | |  ||||||        ||| |||||||| ||||||||||| ||||||||||||||||| || || |||||||| || |||||||||||||| |||||||||||||||| |||||| ||  | |
gtttgtactgttctattcttt--gtttcctcaccttttaagatctgctaattaaattcttactagtcaatacctaccactaatcgtatttaatttattctttcatgattgttaagGTTCGAGTGTTCTACTCTGTGAGAATCTTTCTTGGCCTTATATCAACTATAACAGAAACTGTTCTGGTTGTTGCTCTTTCAAGAAAATATGGAAAAAGAC
















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|28909967|gb|CB331189.1|CB331189
EST:     TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG                         GCTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
genomic: TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
EST: gi|148995029|gb|EE034347.2|EE034347
EST:     TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG                         GTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
genomic: TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
EST: gi|211188227|gb|FK983678.1|FK983678
EST:     TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG                         GTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
genomic: TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
EST: gi|76281865|gb|DV021433.1|DV021433
EST:     TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG                         GTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
genomic: TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
EST: gi|211188228|gb|FK983679.1|FK983679
EST:     TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG                         GTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
genomic: TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
EST: gi|211188231|gb|FK983682.1|FK983682
EST:     TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG                         GTTCGTGTGTTCTACTCAGTGAGAATCTTTTCTGGGTCTCATTTCAACTAT
genomic: TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTT-CTTGGTCTCATTTCAACTAT
EST: gi|74233286|gb|DT641200.1|DT641200
EST:     TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG                         GTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
genomic: TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
EST: gi|211188225|gb|FK983676.1|FK983676
EST:     TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG                         GTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
genomic: TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
EST: gi|71772097|gb|DR970034.1|DR970034
EST:     TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG                         GTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
genomic: TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
EST: gi|211188230|gb|FK983681.1|FK983681
EST:     TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG                         GTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
genomic: TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
EST: gi|211190621|gb|FK983684.1|FK983684
EST:     TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG                         GTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
genomic: TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
EST: gi|91054950|gb|EB165368.1|EB165368
EST:     TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG                         GTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
genomic: TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
EST: gi|149100385|gb|EE186457.2|EE186457
EST:     TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG                         GTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
genomic: TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT
EST: gi|211190622|gb|FK983685.1|FK983685
EST:     TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG                         GTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCA-CTATT
genomic: TTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATT

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 200

TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATTACCGAAACTGTTCTGGTGGTTGCTCTTTCAAGAAGATATGGGAAGCGGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 97

TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATTACCGAAACTGTTCTGGTGGTTGCTCTTTCAAGAAGATATGGGAAGCGGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 107

TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATTACCGAAACTGTTCTGGTGGTTGCTCTTTCAAGAAGATATGGGAAGCGGC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 203

TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAGgtttgtgctc ... tgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATTACCGAAACTGTTCTGGTGGTTGCTCTTTCAAGAAGATATGGGAAGCGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatccctttacctatttgtgcttactaatgatatctcacctattctgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATTACCGAAACTGTTCTGGTGGTTGCTCTTTCAAGAAGATATGGGAAGCGGC
                                      cctattct  CT-rich tract
                         taatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgctctcttactcctttggtttcttcacatccttatatgctggctatccctttacctatttgtgcttactaatgatatctcacctattctgctgtgaagGTTCGTGTGTTCTACTCAGTGAGAATCTTTCTTGGTCTCATTTCAACTATTACCGAAACTGTTCTGGTGGTTGCTCTTTCAAGAAGATATGGGAAGCGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG