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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaggcctgtggccgtctattggaagaagaaaaacagattgtaaatgacaatgtcttatatcctttagaatgaactgtgcctaaggatgagtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGCAATGGTGAATCAGAGCCTGTAACTGAAGCATGTGTACAATTGACCCAAG

Basic information

species Zea mays
transcript GRMZM2G066051_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066051_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 1
------agaggcctgtggccgtctattggaagaagaaaaacagattgtaaatgacaatgtcttatatcctttagaatgaactgtgcctaaggatgagtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGCAATGGTGAATCAGAGCCTGTAACTGAAGCATGTGTACAATTGACCCAAG
        |    || | |  | ||||     || || | || || | |  ||| ||     ||||| | |     | |   |   |||||     ||||||||||||| ||||  |||||||||||||||||||  ||||||| || ||||| |||||||||||||| || ||||| ||||| || || || |||||||||||||
tattatgaatttttgggtcaatttattctgtaaacaata-catat-gaacttgaaaaa----tatattcctatatgttatgggcagctaagaccatgtttatgcagATGGCAGAATTAAGCAAAAATATCAGGGAGTTGAAGTCAATTCTTTATGGCAATGGTGAATCTGAACCTGTGACTGAGGCTTGCGTGCAATTGACCCAAG
















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|149041352|gb|EE046990.2|EE046990
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|148999214|gb|EE036133.2|EE036133
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|78107219|gb|DV525637.1|DV525637
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|149072876|gb|EE161132.2|EE161132
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|149104773|gb|EE290233.2|EE290233
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|6194845|gb|AW146949.1|AW146949
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|149084269|gb|EE173698.2|EE173698
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|71447694|gb|DR828744.1|DR828744
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|148955827|gb|EC901514.2|EC901514
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|71328881|gb|DR801123.1|DR801123
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGC-AAAATATCGGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|31354689|gb|CD439046.1|CD439046
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|60340162|gb|DN207135.1|DN207135
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|32856027|gb|CD995708.1|CD995708
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|149082296|gb|EE171481.2|EE171481
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|6994177|gb|AW453391.1|AW453391
EST:     CTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: CTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|6022524|gb|AW067557.1|AW067557
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|6194848|gb|AW146952.1|AW146952
EST:     ACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: ACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|71447693|gb|DR828743.1|DR828743
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACCGAGCTAAGCCAAAATATCTGGGATATGAAGTCTATCCCTTTACGG
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCC-TTTACGG
EST: gi|149079796|gb|EE168794.2|EE168794
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
EST: gi|149013854|gb|EE043335.2|EE043335
EST:     TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAG                         ATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC
genomic: TCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGC

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: 43 (upstream exon), 47 (downstream exon)
Score: 70

GCGGACGCCCGTGGACATCGTGCGGCAGACGCGCGAGTGCCTCGTCTACCTCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGCAATGGTGAATCAGAGCCTGTAACTGAAGCATGTGTACAATTGACCCAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 120

GCGGACGCCCGTGGACATCGTGCGGCAGACGCGCGAGTGCCTCGTCTACCTCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGCAATGGTGAATCAGAGCCTGTAACTGAAGCATGTGTACAATTGACCCAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 60

GCGGACGCCCGTGGACATCGTGCGGCAGACGCGCGAGTGCCTCGTCTACCTCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGCAATGGTGAATCAGAGCCTGTAACTGAAGCATGTGTACAATTGACCCAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 87

GCGGACGCCCGTGGACATCGTGCGGCAGACGCGCGAGTGCCTCGTCTACCTCGACCTCCACTCGGACTCCAGGAGCGGCGATGCCAAGCGCGAGGAGAAGgtgagatcgg ... gtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGCAATGGTGAATCAGAGCCTGTAACTGAAGCATGTGTACAATTGACCCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacaatgtcttatatcctttagaatgaactgtgcctaaggatgagtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGCAATGGTGAATCAGAGCCTGTAACTGAAGCATGTGTACAATTGACCCAAG
        tcttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaggcctgtggccgtctattggaagaagaaaaacagattgtaaatgacaatgtcttatatcctttagaatgaactgtgcctaaggatgagtttatgcagATGACAGAGCTAAGCAAAAATATCAGGGATATGAAGTCTATCCTTTACGGCAATGGTGAATCAGAGCCTGTAACTGAAGCATGTGTACAATTGACCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - ctgtggc
- - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaactg