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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGCTACAAGTACAGCGGCGTCGACCACTCGCTCGTCGCCAAGTACATCCTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcctcctctcccgttcccccctctctctttggttattgcttctccgtccgtgctctccgttgccaaatgcgtcttgcgagcgattggttttcc...

Basic information

species Zea mays
transcript GRMZM2G466281_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G466281_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g02750.4 (Oryza sativa), 5'ss of exon 1
GGCGCTACAAGTACAGCGGCGTCGACCACTCGCTCGTCGCCAAGTACATCCTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcctcctctcccg---ttcccccctctctctttggttattgcttctccgtccgtgctctccgttgccaaatgcgtcttgcgagcgattggttttcc---
|| | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||| |||||||||| ||||||||||||||  |   | | | ||   |||   ||| ||  |||  ||  | |   |||  | ||| |     |||     ||| |  | | |||   ||| ||||    
GGAGGTACAAGTACAGCGGCGTCGACCACTCGCTCGTCGCCAAGTACATCCTCCAGCCCTTCTGGTCACGATTCGTCAACCTCTTCCCGCTCTGGTTCCCgtaagcgccgcgccccctcgaatttctttcctttccttttcttttcttccattccaccagtgtt-----ttgatccgtgccttgt-caagctcctggctttcgcca
















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|211250318|gb|FL201841.1|FL201841
EST:     TCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTTSCC                         ACCGAACATG
genomic: TCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTC-CCgtaagccgcc ... tgatctgcagACCGAACATG
EST: gi|101388019|gb|EB816024.1|EB816024
EST:     CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCC                         ACCGAACATG
genomic: CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG
EST: gi|76933447|gb|DV173462.1|DV173462
EST:     CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCC                         ACCGAACATG
genomic: CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG
EST: gi|78108358|gb|DV526776.1|DV526776
EST:     CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCC                         ACCGAACATG
genomic: CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG
EST: gi|76284393|gb|DV023961.1|DV023961
EST:     CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCC                         ACCGAACATG
genomic: CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG
EST: gi|211250321|gb|FL201844.1|FL201844
EST:     CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCC                         ACCGAACATG
genomic: CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG
EST: gi|211250315|gb|FL201838.1|FL201838
EST:     CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCC                         ACCGAACATG
genomic: CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG
EST: gi|148930548|gb|EE285169.2|EE285169
EST:     CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCC                         ACCGAACATG
genomic: CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG
EST: gi|148948015|gb|EC893516.2|EC893516
EST:     CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCC                         ACCGAACATG
genomic: CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG
EST: gi|149095953|gb|EE181619.2|EE181619
EST:     CTCCAGGCCTTCTGGTCCCGATTCGACAACATCTTCCCGCTACGCTTCCC                         ACCGAACATG
genomic: CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG
EST: gi|211250319|gb|FL201842.1|FL201842
EST:     CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCC                         ACCGAACATG
genomic: CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG
EST: gi|149085392|gb|EE174899.2|EE174899
EST:     CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCC                         ACCGAACATG
genomic: CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG
EST: gi|88756189|gb|DY540330.1|DY540330
EST:     CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCC                         ACCGAACATG
genomic: CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG
EST: gi|211250320|gb|FL201843.1|FL201843
EST:     CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTTCC                         ACNNAACATG
genomic: CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG
EST: gi|88756155|gb|DY540296.1|DY540296
EST:     CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCC                         ACCGAACATG
genomic: CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG
EST: gi|211250316|gb|FL201839.1|FL201839
EST:     CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTKNCC                         ACCGAACATG
genomic: CTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG

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), 10 (downstream exon)
Score: 130

GGCGCTACAAGTACAGCGGCGTCGACCACTCGCTCGTCGCCAAGTACATCCTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG


Block sizes: 49 (upstream exon), 10 (downstream exon)
Score: 122

GGCGCTACAAGTACAGCGGCGTCGACCACTCGCTCGTCGCCAAGTACATCCTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG


Block sizes: 49 (upstream exon), 10 (downstream exon)
Score: 102

GGCGCTACAAGTACAGCGGCGTCGACCACTCGCTCGTCGCCAAGTACATCCTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG


Block sizes: 49 (upstream exon), 10 (downstream exon)
Score: 209

GGCGCTACAAGTACAGCGGCGTCGACCACTCGCTCGTCGCCAAGTACATCCTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcc ... tgatctgcagACCGAACATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGCTACAAGTACAGCGGCGTCGACCACTCGCTCGTCGCCAAGTACATCCTCCAGCCCTTCTGGTCCCGATTCGTCAACATCTTCCCGCTATGGTTCCCgtaagccgcctcctctcccgttcccccctctctctttggttattgcttctccgtccgtgctctccgttgccaaatgcgtcttgcgagcgattggttttcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccgtcc