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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataattgtcaatcatgtagttttctctttcgacataagcaatcatgtatttgtagttgctttaccactatactgaaaattcattaaaatattttgttcagGGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGAT

Basic information

species Zea mays
transcript GRMZM2G014454_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014454_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g62070.2 (Oryza sativa), 3'ss of exon 3
ataattgtcaatcatgtagttttctctttcgacataagcaatcatgtatttgtagttgctttac--cactatactgaaaattc-attaaaatattttgttcagGGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGAT
|| ||| | | || || | || | || |||| | || || | | | || ||| ||| ||| || | ||||| || |||||||||||||||| ||||| ||||||||||| || |||||||||||||| || |||||||||||||| || ||| ||||||||
--tcgagtttatcgcttc-tcttttcacttagtattatcagtcatacacttttaagttccaaatttcaatatgttgactgttccatcacaatatcttcttcagGGAATACTTGTCTTTGCCTCTGTTATGGCGACACTTGGCCTTCAGATCATCCTAGAATCAGTACGCTCGTTGTTGTCTGAT

upper sequence: GRMZM2G014454_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G52280.1 (Glycine max), 3'ss of exon 3
ataattgtcaatcatgtagttttctctttcgacataagcaa-tcatgtatttgtagttgctttaccactatactgaaaattc-attaaaatattttgttcagGGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGAT
|| | | || |||| | || | | | | | || | | || | || | |||| | || | | || |||| || |||||||| ||||||||||| ||||||||||| || ||||| || |||||||| | || || || |||| | ||| |
-aaactataaagtgaa-agttcattattaaattgttaatggcttaacgagttattatgactgtgccttggtgctgagattttgaattcaaaatttggtacagGGAATTCTTGTTTTTGCCTCTGTTATGGCGACACTTGGACTGCAGATAATCTTGGAGTCTACCCGCACATTAATATCTTCT

upper sequence: GRMZM2G014454_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G10580.1 (Glycine max), 3'ss of exon 3
ataattgtcaatcatgtagttttctctttcgacataagcaatcatgtat-ttgtagttgctttaccactatactgaaaattc-attaaaatattttgttcagGGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGAT
|| | | | | | | || | | | || | | || | || | |||| | || | | || |||| || |||||||| ||||||||||| ||||||||||| || ||||| || |||||||| | || || || |||| | ||| |
--aacttcgtaccccattgcccattattaaatagctaatggcctaacaagttattatgactgtgccttggtgctgagattttgaattcaaaatttggtacagGGAATTCTTGTTTTTGCCTCTGTTATGGCGACACTTGGACTGCAGATAATCTTGGAGTCTACCCGCACATTAATATCTTCT

upper sequence: GRMZM2G014454_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0019g00020.t01 (Vitis vinifera), 3'ss of exon 3
----ataattgtcaatcatgtagttttctctttcgacataagcaatcatgtatttgtagttgctttaccactatactgaaaattcattaaaatattttgttcagGGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGAT
|| | | ||| | |||| || ||| | | | || || || ||| | | ||| | | ||| |||||||| |||||||||||||||||||||||||| || || || |||||||| | || |||||||| || | |||||
tgctgcaaaaatagagcatttggtttctagaatcctggaaagtgtctttttctgggttgtgatattgttactgaagccttgaatcaccat----tgatgtgcagGGAATCCTTGTTTTTGCTTCTGTTATGGCAACTCTGGGACTGCAGATAATCTTGGAGTCAGTACGCACACTATCATCTGAC

upper sequence: GRMZM2G014454_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S11_299V6.2 (Physcomitrella patens), 3'ss of exon 4
ataattgtcaatcatgtagttttctctttcgacataagcaatcatgtatttgtagttgctttaccactatactgaaaattcattaaaatattttgtt-----cagGGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGAT
| | | || || | | | || | | | || || || | | || || || | || | | | || ||||| || || ||||||||||| || |||||||| ||||| ||||| || ||||||||||| ||||| | | | || |
----taaagttttttctacccttataacatgtctgcagttgatacatgtctgcagaaa-ttcatcgttactaaaaagataccttttgttttctgcttggcgacagGGTATTCTGGTTTTTGCTTCAGTAATGGCAACACTTGGTCTTCAAATCATTCTAGAATCCGTACGGACTCTAATCACTCAG

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|91050036|gb|EB160454.1|EB160454
EST:     CACCAAATCCATACAGATACCCAATTGGGAAAAAGCGGATGCAGCCACTG                         GGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATT
genomic: CACCAAATCCATACAGATACCCAATTGGGAAAAAGCGGATGCAGCCACTGgtgagttttt ... ttttgttcagGGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATT
EST: gi|91056110|gb|EB166528.1|EB166528
EST:     CACCAAATCCATACAGATACCCAATTGGGAAAAAGCGGATGCAGCCACTG                         GGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATT
genomic: CACCAAATCCATACAGATACCCAATTGGGAAAAAGCGGATGCAGCCACTGgtgagttttt ... ttttgttcagGGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATT
EST: gi|148945796|gb|EC891082.2|EC891082
EST:     CACCAAATCCATACAGATACCCAATTGGGAAAAAGCGGATGCAGCCACTG                         GGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATT
genomic: CACCAAATCCATACAGATACCCAATTGGGAAAAAGCGGATGCAGCCACTGgtgagttttt ... ttttgttcagGGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATT

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), 38 (downstream exon)
Score: 24

AGACTTGTTGTCAGGATTTATCTTGTGGTTTACTGCCTTTTCAATGCAAACACCAAATCCATACAGATACCCAATTGGGAAAAAGCGGATGCAGCCACTGgtgagttttt ... ttttgttcagGGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

AGACTTGTTGTCAGGATTTATCTTGTGGTTTACTGCCTTTTCAATGCAAACACCAAATCCATACAGATACCCAATTGGGAAAAAGCGGATGCAGCCACTGgtgagttttt ... ttttgttcagGGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

AGACTTGTTGTCAGGATTTATCTTGTGGTTTACTGCCTTTTCAATGCAAACACCAAATCCATACAGATACCCAATTGGGAAAAAGCGGATGCAGCCACTGgtgagttttt ... ttttgttcagGGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

AGACTTGTTGTCAGGATTTATCTTGTGGTTTACTGCCTTTTCAATGCAAACACCAAATCCATACAGATACCCAATTGGGAAAAAGCGGATGCAGCCACTGgtgagttttt ... ttttgttcagGGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatttgtagttgctttaccactatactgaaaattcattaaaatattttgttcagGGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGAT
                                             ttttgttc  CT-rich tract
 tatactgaaaattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataattgtcaatcatgtagttttctctttcgacataagcaatcatgtatttgtagttgctttaccactatactgaaaattcattaaaatattttgttcagGGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGAT

- - - - - - catgtag
- - - - - - - - - - - - - - - - - - - - - catgtat