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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatttcacgagtatctctttagtgcatttgtattttctctatcagtttttttggacattatattttttctgtacttctaaaagttgccttatac...

Basic information

species Zea mays
transcript GRMZM2G134613_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134613_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g09240.1 (Oryza sativa), 5'ss of exon 4
GTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatttcacgagtatctctttag--tgcatttg----tattttctctatcagtttttttggacattatattttttctgtacttctaaaagttgccttatac
||||||||||||||||| |||||||||||||| || ||||||||||| || |||||||   |    |   |  || || ||  |  || |      | ||| ||| |   | |||| | |  |||| ||    ||  | || | |  | |||       
GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagttctcaaccattttacttttaagaataaatctagtgccactttatctctatttgttttggcaagttatgttgacacttcattttttat-gctgctg-----

upper sequence: GRMZM2G134613_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S249_49V6.2 (Physcomitrella patens), 5'ss of exon 3
-----------------------------------------------GTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatttcacgagtatctctttagtgcatttg-tatt-ttctctatcagtttttttggac---attatattttttctgtact-tctaaaagttgccttatac-------------------------------------------------------------
                                               || ||||| ||||| ||||| | |||||||||| ||||||| |||||||||||||  |   |||      | | | | ||  |   |||  ||| || ||  |   | |||| ||      |   |||  ||  ||  | | |      |   | ||                                                               
AAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAATTCCTGTAATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGACAAGAAAAAgtatgtagtttgt--gttctttttgtaacgagcttgacattattttcctttcatattttggggttgagtctgattggtttcgttttgtttggggcctaaataattttagttcgtgcgcactgaattgtggcacgttctttgaattgatatgaggaacgcctgtgtag
















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|116828492|gb|EC857917.1|EC857917
EST:     ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAA                         GTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
genomic: ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
EST: gi|16921805|gb|BM075308.1|BM075308
EST:     ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAA                         GTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
genomic: ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
EST: gi|71306764|gb|DR789543.1|DR789543
EST:     ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAA                         GTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
genomic: ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
EST: gi|71306765|gb|DR789544.1|DR789544
EST:     ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAA                         GTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
genomic: ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
EST: gi|37386976|gb|CF630680.1|CF630680
EST:     ATTGTTGAGAAGGCCGTGAGGAGTGACATCCCAGACATTGACAAGAAAAA                         GTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
genomic: ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
EST: gi|16925527|gb|BM078595.1|BM078595
EST:     ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAA                         GTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
genomic: ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
EST: gi|67025573|gb|CO454322.1|CO454322
EST:     ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAA                         GTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
genomic: ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
EST: gi|84980814|gb|DW531163.1|DW531163
EST:     ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAA                         GTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
genomic: ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
EST: gi|5761920|gb|AI966893.1|AI966893
EST:     ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAA                         GTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
genomic: ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
EST: gi|116815633|gb|EC858313.1|EC858313
EST:     TTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGCACATTGACAAGACAAA                         GTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
genomic: TTGTTGAGAAGGCCGAGAGGAGTGACATCCCAG-ACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
EST: gi|211145629|gb|FL256802.1|FL256802
EST:     ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAA                         GTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
genomic: ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
EST: gi|18168853|gb|BM338693.1|BM338693
EST:     ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAA                         G
genomic: ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcag-
EST: gi|18168853|gb|BM338693.1|BM338693
EST:     ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAA                         G
genomic: ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcag-
EST: gi|37374696|gb|CF623730.1|CF623730
EST:     ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAA                         GTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
genomic: ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
EST: gi|67040113|gb|CO466368.1|CO466368
EST:     ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAA                         GTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG
genomic: ATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACG

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), 45 (downstream exon)
Score: 79

GTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACGGAAGCGGATCAAGCTCAGCGCTGAGAAGGCAATCTTCATCTTCGTAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 447

GTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACGGAAGCGGATCAAGCTCAGCGCTGAGAAGGCAATCTTCATCTTCGTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 485

GTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACGGAAGCGGATCAAGCTCAGCGCTGAGAAGGCAATCTTCATCTTCGTAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 288

GTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatt ... ttgcttgcagGTACCTTGTTCCTGCCGACCTCACAGTCGGACAGTTTGTGTATGTGGTACGGAAGCGGATCAAGCTCAGCGCTGAGAAGGCAATCTTCATCTTCGTAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATTGTTGAGAAGGCCGAGAGGAGTGACATCCCAGACATTGACAAGAAAAAgtcagccatttcacgagtatctctttagtgcatttgtattttctctatcagtttttttggacattatattttttctgtacttctaaaagttgccttatac

- - - - - - - - - GAGAGG
- - - - - - - - -  AGAGGA
- - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - -  AAGAAA