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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgtgtgtgcaatcgatctatatatgtgtgtggaaaggagaggaatgggatgagctaatataattgtctgggaaaaaaaaaaaccatatatgtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTGCTGTACAAGGAGGAGCTGGAGAAGATGAAGGAGATGGCGCCGGACAACT

Basic information

species Zea mays
transcript GRMZM2G059191_T01
intron # 5
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|16378028|gb|BI992251.1|BI992251
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|71762625|gb|DR960562.1|DR960562
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|71432261|gb|DR813311.1|DR813311
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|149073444|gb|EE161749.2|EE161749
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|71297722|gb|DR784813.1|DR784813
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|71763164|gb|DR961101.1|DR961101
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|149073700|gb|EE162006.2|EE162006
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTTTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|71306720|gb|DR789520.1|DR789520
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|148962439|gb|EE013294.2|EE013294
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|91876931|gb|EB406888.1|EB406888
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|76019472|gb|DT946642.1|DT946642
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|71313358|gb|DR793225.1|DR793225
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|94475953|gb|EB704911.1|EB704911
EST:     GAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: GAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|71436411|gb|DR817461.1|DR817461
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|4730332|gb|AI649498.1|AI649498
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|89248692|gb|DY620478.1|DY620478
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|71307167|gb|DR789753.1|DR789753
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|76283319|gb|DV022887.1|DV022887
EST:     GGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: GGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|5928946|gb|AW056238.1|AW056238
EST:     TCCGCTCCTTCCTGTGGAAGATGTTCCTAGAGGAGCACGAGGACTACAAG                         TTCACCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|13178509|gb|BG349767.1|BG349767
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|71326435|gb|DR799900.1|DR799900
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|71428874|gb|DR809924.1|DR809924
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCTTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|13125967|gb|BG316642.1|BG316642
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|94479916|gb|EB708874.1|EB708874
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|13315903|gb|BG410251.1|BG410251
EST:     TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
EST: gi|110219228|gb|EC901126.1|EC901126
EST:     TCCGCTCCTTTTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAG                         TTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG
genomic: TCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTG

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: 37 (upstream exon), 28 (downstream exon)
Score: 4

CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTGCTGTACAAGGAGGAGCTGGAGAAGATGAAGGAGATGGCGCCGGACAACT


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 133

CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTGCTGTACAAGGAGGAGCTGGAGAAGATGAAGGAGATGGCGCCGGACAACT


Block sizes: 47 (upstream exon), 21 (downstream exon)
Score: 5

CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTGCTGTACAAGGAGGAGCTGGAGAAGATGAAGGAGATGGCGCCGGACAACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 165

CTCGCAACGGGGACCGGTATTGCTCCGTTCCGCTCCTTCTTGTGGAAGATGTTCCTGGAGGAGCACGAGGACTACAAGgtgtgtgtgt ... gtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTGCTGTACAAGGAGGAGCTGGAGAAGATGAAGGAGATGGCGCCGGACAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggatgagctaatataattgtctgggaaaaaaaaaaaccatatatgtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTGCTGTACAAGGAGGAGCTGGAGAAGATGAAGGAGATGGCGCCGGACAACT
      agctaat  putative branch site (score: 165)
                          aaaaaaaaaaaccata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgtgtgtgcaatcgatctatatatgtgtgtggaaaggagaggaatgggatgagctaatataattgtctgggaaaaaaaaaaaccatatatgtattaacagTTCAGCGGCCTTGCGTGGCTGTTCTTGGGAGTCCCGACGAGCGACAGCCTGCTGTACAAGGAGGAGCTGGAGAAGATGAAGGAGATGGCGCCGGACAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG