Skip to another splice site:
1  
 5'  3'   
2  
 5'  3'   
3  
 5'  3'   
4  
 5'  3'   
5  
 5'  3'   
6  
 5'  3'   
7  
 5'  3'   
8  
 5'  3'   
9  
 5'  3'   
10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaaaagttaattgcccttttaacctacattacgatttacgaggatacaattttgttttacaaatgtagacacactaatgtccttcctcttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCAGTCAATCCTGTCCAGGCTGCACAAGCAGCTCAAACTGCAGCTCCATCTG

Basic information

species Zea mays
transcript GRMZM2G105772_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105772_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g24200.2 (Oryza sativa), 3'ss of exon 6
gttaaaagttaattgcccttttaacctacattacgatttacg----aggatacaattttgttttacaaatgtagacacactaatgtcctt--cctcttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCAGTCAATCCTGTCCAGGCTGCACAAGCAGCTCAAACTGCAGCTCCATCTG
| | || | | || | ||| || | | || | || | | ||| | || | |||||||| ||||| | ||| | ||||| ||||||| || ||||| |||| ||||||||||||| ||||||| ||||||| ||||||| |||| ||| ||||| | |||||||||||
aatcgtatgtagtattctacagaaaatgcatgttgactcaaactttagattgcagatatttttggc---tgca---acactaatatccttgtctgctttaatgtagGGTGTTCCTGAGCAGATGGACATTCCAGTTCCACCTCCGAGTATACAGCCAGCCAATCCTACCCAGGCTTCACAGGCAACTCAACCAGCAGCTCCATCAA
















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|31364335|gb|CD448690.1|CD448690
EST:     TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGATGTTCCTACATCAGCTCCGAGTATCCAGCCA
genomic: TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCA
EST: gi|148969759|gb|EE020640.2|EE020640
EST:     TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCA
genomic: TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCA
EST: gi|60396086|gb|DN228955.1|DN228955
EST:     TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCG
genomic: TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCG
EST: gi|78118533|gb|DV536917.1|DV536917
EST:     TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCA
genomic: TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCA
EST: gi|148991633|gb|EE033168.2|EE033168
EST:     TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAA
genomic: TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAA
EST: gi|91876143|gb|EB406100.1|EB406100
EST:     TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGATGTTCCTACATCACCT
genomic: TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCT
EST: gi|74240960|gb|DT648874.1|DT648874
EST:     TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAG
genomic: TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAG
EST: gi|76011555|gb|DT938725.1|DT938725
EST:     TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCT                         GGGATTCCTGNAACAA-TGGATGTTCCTACATCACCTCCGAGTATCCAGCC
genomic: TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTG-AACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCC
EST: gi|148956696|gb|EC902566.2|EC902566
EST:     TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCA
genomic: TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCA
EST: gi|149001065|gb|EE038319.2|EE038319
EST:     TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGATGTTCCCTACATCACCTCCGAGTATCCAGCC
genomic: TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGATGTTCC-TACATCACCTCCGAGTATCCAGCC
EST: gi|91057192|gb|EB167610.1|EB167610
EST:     TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCA
genomic: TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCA
EST: gi|149096952|gb|EE182751.2|EE182751
EST:     TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCT                         GGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCA
genomic: TGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCA

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: 148

TCTTGAAATGGGTGGCGGGATATGGGACAGAGACACTGTACTACGTGCCCTGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCAGTCAATCCTGTCCAGGCTGCACAAGCAGCTCAAACTGCAGCTCCATCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

TCTTGAAATGGGTGGCGGGATATGGGACAGAGACACTGTACTACGTGCCCTGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCAGTCAATCCTGTCCAGGCTGCACAAGCAGCTCAAACTGCAGCTCCATCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

TCTTGAAATGGGTGGCGGGATATGGGACAGAGACACTGTACTACGTGCCCTGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCAGTCAATCCTGTCCAGGCTGCACAAGCAGCTCAAACTGCAGCTCCATCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

TCTTGAAATGGGTGGCGGGATATGGGACAGAGACACTGTACTACGTGCCCTGCGGGTTGCGTATAACAACCCAGAGCGCGCTGTTGAGTACTTATATTCTgtaagaatga ... ttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCAGTCAATCCTGTCCAGGCTGCACAAGCAGCTCAAACTGCAGCTCCATCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacaattttgttttacaaatgtagacacactaatgtccttcctcttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCAGTCAATCCTGTCCAGGCTGCACAAGCAGCTCAAACTGCAGCTCCATCTG
                            cactaat  putative branch site (score: 81)
 tgtccttcctcttctg  CT-rich tract
 attttgttttacaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaaagttaattgcccttttaacctacattacgatttacgaggatacaattttgttttacaaatgtagacacactaatgtccttcctcttctgtttagGGGATTCCTGAACAAATGGATGTTCCTACATCACCTCCGAGTATCCAGCCAGTCAATCCTGTCCAGGCTGCACAAGCAGCTCAAACTGCAGCTCCATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC