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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgctccctttttttcccctcatgcagtgtcgtgcctcgtttcctgtggtgtatgaggatgattccattcactcgtgcgtgctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCTCTCAACGAG

Basic information

species Zea mays
transcript GRMZM2G168176_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168176_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g37870.1 (Oryza sativa), 3'ss of exon 1
---------------gtgagtgctccctttttttcccctca-tgcagtgtcgtgcctcgtt--tcctgtggtgtatgaggatgattccattc------------actcgtgcgtgctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCTCTCAACGAG
                 | | ||||  ||||||| |  ||  ||   ||| | | |   |   ||   || ||| ||    || |    ||               | ||| ||  |   ||||||||||| |||||||||||| ||||| ||||| |||| |||||||| |||||||||||||||||||||||||||||||||||||| || || |||||||||
gtgagtggcgccgcaccgcgcgctcgtttttttttcgttcggtgtgatgtggcggcggatagatcgattgatgtgtggatgtgttgtttttgtggggggattggggtggtgggttttgctcgtagGTATCGGCATCTGATGCAGAACGTGGTGTCGCTGCTGCCGCACGCCAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGCAATGCGCTCAACGAG
















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|101388447|gb|EB816210.1|EB816210
EST:     AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAG                         GTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
genomic: AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
EST: gi|211512372|gb|FL212647.1|FL212647
EST:     AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAG                         GTATCGTCATCTGATGCAGGACGTGCTGTCGATGCTCCCGCACGCGAAGAA
genomic: AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
EST: gi|13198570|gb|BG354387.1|BG354387
EST:     AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAG                         GTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACG
genomic: AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACG
EST: gi|148943696|gb|EC888763.2|EC888763
EST:     AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAG                         GTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
genomic: AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
EST: gi|76289778|gb|DV029346.1|DV029346
EST:     AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAG                         GTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
genomic: AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
EST: gi|76285403|gb|DV024971.1|DV024971
EST:     AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAG                         GTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
genomic: AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
EST: gi|71325419|gb|DR799392.1|DR799392
EST:     AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAG                         GTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
genomic: AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
EST: gi|71307148|gb|DR789745.1|DR789745
EST:     AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAG                         GTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
genomic: AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
EST: gi|28930902|gb|CB334263.1|CB334263
EST:     AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAG                         GTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
genomic: AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
EST: gi|78121527|gb|DV539911.1|DV539911
EST:     AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAG                         GTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
genomic: AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
EST: gi|89759058|gb|DY688001.1|DY688001
EST:     AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAG                         GTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
genomic: AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
EST: gi|6827088|gb|AW330731.1|AW330731
EST:     CCCGCCGCATCACGTACAG                         GTATCGTCATCTGATGCAGGACGTGCTATCGATGCTCCCGCACGCGAAGAA
genomic: CCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
EST: gi|76283913|gb|DV023481.1|DV023481
EST:     AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAG                         GTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
genomic: AGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA
EST: gi|78180563|gb|DV550891.1|DV550891
EST:     TACTCATCACCTGCTCCCGCCGCATCACGTACAG                         GTATCGTCATCTGATGCAGGACGTGCTATCGATGCTCCCGCACGCGAAGAA
genomic: TACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAA

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), 49 (downstream exon)
Score: 288

CCGACGCCGTGCCTGACTCCGCGGCCTCCAGGGCCGCGGTGGCGCCGTTTAGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCTCTCAACGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 121

CCGACGCCGTGCCTGACTCCGCGGCCTCCAGGGCCGCGGTGGCGCCGTTTAGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCTCTCAACGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 202

CCGACGCCGTGCCTGACTCCGCGGCCTCCAGGGCCGCGGTGGCGCCGTTTAGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCTCTCAACGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 102

CCGACGCCGTGCCTGACTCCGCGGCCTCCAGGGCCGCGGTGGCGCCGTTTAGGAACAGGGAGAAGGTACTCATCACCTGCTCCCGCCGCATCACGTACAGgtgagtgctc ... ctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCTCTCAACGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgctccctttttttcccctcatgcagtgtcgtgcctcgtttcctgtggtgtatgaggatgattccattcactcgtgcgtgctcgacgtagGTATCGTCATCTGATGCAGGACGTGTTGTCGATGCTCCCGCACGCGAAGAAGGACAGCAAGGTCGAGTCGAAGCAGAGCAAGGGGAACGCTCTCAACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG