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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGACCGGGATGATCTACCTGATCAGGGCAGTGGTCACTTTGCTGAAACAGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagacatgtacctcactgtatgcttggctacttgaatgttagtatggagttggtcaccggccctgtcagttaatacattaaccattccatatgctgtacccttgctactaattttgcag

Basic information

species Zea mays
transcript GRMZM2G071714_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071714_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g38330.1 (Oryza sativa), 5'ss of exon 2
GTTGACCGGGATGATCTACCTGATCAGGGCAGTGGTCACTTTGCTGAAACAGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagacatgtacctcactgtatgcttggctacttgaatgttagtatggagttggtcaccggccctgtcagttaatacattaaccattccatatgctgtaccctt--gctactaattttgcag
|||||||| |||||| |||||||||| || ||||||||||||||||||||||| || ||||||||||  |||||||||||||||||||||||||| ||||||||| ||||| |  ||       ||||| | || | |   || |||||    |  |||     | ||||| | ||||    |     |||| |||  |||||||||  || | | |||||||||
GTTGACCGCGATGATTTACCTGATCAAGGGAGTGGTCACTTTGCTGAAACAGTTCAAAAGCTAAAGGTGTTGAAGCCAGAAATGCTTATTGAAGCACTTGgtaagtgacatatttctggtatattgctttgttattcg---gtcagtatattatcagtc-----ctctgtctgctaatgttgtgc---ttccctatattgtacccttatgcaagttattttgcag

upper sequence: GRMZM2G071714_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT2G20860.1 (Arabidopsis thaliana), 5'ss of exon 2
GTTGACCGGGATGATCTACCTGATCAGGGCAGTGGTCACTTTGCTGAAACAGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagacatgtacctcactgtatgcttggctact-tgaatgttagtatggagttggtcaccggccctgtcagttaatacattaaccattccatatgctgtacccttgctactaattttgcag
|| || || |||||| |||||||||| || |||||||| ||||||||||| || ||||   | ||    |||||||| || ||| | |||||||| || ||||| | | ||| | ||    ||  | |||   |   ||| | || || |  | || ||         |||  | | ||  |                                          
GTAGATCGAGATGATTTACCTGATCAAGGGAGTGGTCATTTTGCTGAAACTGTTCAGAGATTGAAATTCTTGAAGCCGGAGATGTTGATTGAAGCACTAGgtaatata-atg-atctg---gtgggattgatcatcatgagttttggtttttaatttgttttg----ttgtttgatgatgtag-----------------------------------------
















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|91872938|gb|EB402895.1|EB402895
EST:     AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTG                         TACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
genomic: AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
EST: gi|149103480|gb|EE288873.2|EE288873
EST:     AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTG                         TACCTGATTTCCGTGGAGATCCAAGCTG
genomic: AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTG
EST: gi|149083380|gb|EE172687.2|EE172687
EST:     AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCACTTG                         TACCTGATTTCCGTGGAGATCCGAGCTGCGTAGAGAAGGTTGCGACTTCTG
genomic: AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
EST: gi|74244797|gb|DT652711.1|DT652711
EST:     AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTG                         TACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
genomic: AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
EST: gi|76011109|gb|DT938279.1|DT938279
EST:     AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTG                         TACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
genomic: AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
EST: gi|149110556|gb|EE190481.2|EE190481
EST:     AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTG                         TACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
genomic: AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
EST: gi|93281869|gb|EB674133.1|EB674133
EST:     AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTG                         TATCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
genomic: AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
EST: gi|93281868|gb|EB674132.1|EB674132
EST:     AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTG                         TATCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
genomic: AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
EST: gi|71313819|gb|DR793500.1|DR793500
EST:     AGTACAGAAGCTAAAGGTTTTGAAGCCAGAAATGCTTATTGAAGCGCTTG                         TACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
genomic: AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
EST: gi|78113555|gb|DV531946.1|DV531946
EST:     AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTG                         TACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
genomic: AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
EST: gi|74244796|gb|DT652710.1|DT652710
EST:     AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTG                         TACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
genomic: AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
EST: gi|71313820|gb|DR793501.1|DR793501
EST:     AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTG                         TACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
genomic: AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
EST: gi|91875685|gb|EB405642.1|EB405642
EST:     AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTG                         TACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAGGGTTGCGACTTCTG
genomic: AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
EST: gi|71300477|gb|DR786296.1|DR786296
EST:     AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTG                         TACCTGATTTTCGTGGAGATCCAAGCTGCGTAGAAGA-GGTTGCGACTTCT
genomic: AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGA-GAAGGTTGCGACTTCT
EST: gi|74244354|gb|DT652268.1|DT652268
EST:     AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTG                         TACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG
genomic: AGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTG

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: 46 (upstream exon), 47 (downstream exon)
Score: 106

GTTGACCGGGATGATCTACCTGATCAGGGCAGTGGTCACTTTGCTGAAACAGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTGGATTGCATGTTTTTGCGCACAACATTGAAACTGTGGAAGAGCTTCAAAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 109

GTTGACCGGGATGATCTACCTGATCAGGGCAGTGGTCACTTTGCTGAAACAGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTGGATTGCATGTTTTTGCGCACAACATTGAAACTGTGGAAGAGCTTCAAAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 115

GTTGACCGGGATGATCTACCTGATCAGGGCAGTGGTCACTTTGCTGAAACAGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTGGATTGCATGTTTTTGCGCACAACATTGAAACTGTGGAAGAGCTTCAAAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 113

GTTGACCGGGATGATCTACCTGATCAGGGCAGTGGTCACTTTGCTGAAACAGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagaca ... aattttgcagTACCTGATTTCCGTGGAGATCCAAGCTGCGTAGAGAAGGTTGCGACTTCTGGATTGCATGTTTTTGCGCACAACATTGAAACTGTGGAAGAGCTTCAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGACCGGGATGATCTACCTGATCAGGGCAGTGGTCACTTTGCTGAAACAGTACAGAAGCTAAAGGCTTTGAAGCCAGAAATGCTTATTGAAGCGCTTGgtaagagacatgtacctcactgtatgcttggctacttgaatgttagtatggagttggtcaccggccctgtcagttaatacattaaccattccatatgctgtacccttgctactaattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC