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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatatgtgcactatgtgcaccaatcttccatgtgcaacagatatgttctctatcatgatacccttcagtattttcatcactgatgattttctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCTAAGGATGACGATGATGAGAGCGGTGAAGAATATGAAGAGGAAGAGCGTG

Basic information

species Zea mays
transcript GRMZM2G158918_T01
intron # 4
splice site 3'
intron type U2

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|60356594|gb|DN223567.1|DN223567
EST:     AGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATG                         ACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
genomic: AGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
EST: gi|60344122|gb|DN211095.1|DN211095
EST:     AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATG                         ACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
genomic: AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
EST: gi|211512368|gb|FL212178.1|FL212178
EST:     AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATG                         ACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
genomic: AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
EST: gi|211204451|gb|FL397408.1|FL397408
EST:     AATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATG                         ACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
genomic: AATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
EST: gi|211514714|gb|FL212183.1|FL212183
EST:     AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATG                         ACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
genomic: AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
EST: gi|211514718|gb|FL212187.1|FL212187
EST:     AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATG                         ACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
genomic: AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
EST: gi|60337065|gb|DN204038.1|DN204038
EST:     AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATG                         ACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
genomic: AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
EST: gi|60342605|gb|DN209578.1|DN209578
EST:     AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATG                         ACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
genomic: AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
EST: gi|60291784|gb|DN190023.1|DN190023
EST:     AAACAAGTTCAAAAATG                         ACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
genomic: AAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
EST: gi|60355178|gb|DN222151.1|DN222151
EST:     AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATG                         ACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
genomic: AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
EST: gi|60352190|gb|DN219163.1|DN219163
EST:     AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATG                         ACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
genomic: AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
EST: gi|60345474|gb|DN212447.1|DN212447
EST:     AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATG                         ACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
genomic: AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
EST: gi|60400324|gb|DN233131.1|DN233131
EST:     AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATG                         ACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT
genomic: AGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCT

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: 48 (upstream exon), 49 (downstream exon)
Score: 302

GCCCACGATATTTGAAGTAGTGACTGGGGTTGCAAATAAACAAAACAAGGAGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCTAAGGATGACGATGATGAGAGCGGTGAAGAATATGAAGAGGAAGAGCGTG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 121

GCCCACGATATTTGAAGTAGTGACTGGGGTTGCAAATAAACAAAACAAGGAGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCTAAGGATGACGATGATGAGAGCGGTGAAGAATATGAAGAGGAAGAGCGTG


Block sizes: 35 (upstream exon), 42 (downstream exon)
Score: 61

GCCCACGATATTTGAAGTAGTGACTGGGGTTGCAAATAAACAAAACAAGGAGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCTAAGGATGACGATGATGAGAGCGGTGAAGAATATGAAGAGGAAGAGCGTG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 122

GCCCACGATATTTGAAGTAGTGACTGGGGTTGCAAATAAACAAAACAAGGAGAAGGGCCCCAATAGTACCAGCAAAAGCAACAAAACAAGTTCAAAAATGgtaagtttag ... tctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCTAAGGATGACGATGATGAGAGCGGTGAAGAATATGAAGAGGAAGAGCGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctctatcatgatacccttcagtattttcatcactgatgattttctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCTAAGGATGACGATGATGAGAGCGGTGAAGAATATGAAGAGGAAGAGCGTG
                                 cactgat  putative branch site (score: 122)
                                          ttttctgtttc  putative PPT
                        tattttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatatgtgcactatgtgcaccaatcttccatgtgcaacagatatgttctctatcatgatacccttcagtattttcatcactgatgattttctgtttcagACATCAAGACCCGAGTCTCATTCCAAGGCGACAAAAGTGGCAGTGCCCCCTAAGGATGACGATGATGAGAGCGGTGAAGAATATGAAGAGGAAGAGCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- -tatgtgc
- - - - - - - -gtgcacc
- - - - - - - - - - - - - ttccatg
- - - - - - - - - - - - - - - - - gcaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgat