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'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTCAAAACTTTGCCAAGATGTTTGATATCACTTTTGAGAATGAGAAAGGTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctcactcctttgatttaagatgcatcatgcatgattgatgtggggatgggaatgattgctttcattttgtaggctgcacctgatacttttgtcc...

Basic information

species Zea mays
transcript GRMZM2G094123_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094123_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g25710.2 (Oryza sativa), 5'ss of exon 9
TGGTCAAAACTTTGCCAAGATGTTTGATATCACTTTTGAGAATGAGAAAGGTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctcac---tcctttgatttaaga-tgcatcatgcatgattgatgtggggatgggaatgattgctttcattttgtaggctgcacctgatacttttgtcc
||||||||||||||| ||||||||||||||||||||||||||||| || ||    ||    ||||| ||||| ||||||||||| ||||| |||||||||||| ||||||    |  ||  ||||  || || | |  | ||  |     ||          |    |   | || || ||      |  |||  |||||    
TGGTCAAAACTTTGCAAAGATGTTTGATATCACTTTTGAGAATGATAAGGGCTCAAGATCCATGGTGTGGCAGAACTCTTGGGCATACACCACCCGCTCGgtaattctcatatattgttaaattttggaatgtacctggaattttcttcttgttttgcccttttgaagtggtaatgttttacaaaagaaatgaggctttt----

upper sequence: GRMZM2G094123_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT3G62120.2 (Arabidopsis thaliana), 5'ss of exon 8
TGGTCAAAACTTTGCCAAGATGTTTGATATCACTTTTGAGAATGAGAAAGGTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctcactcctttgatttaagatgcatcatgcatgattgatgtggggatgggaa-tgattgctttca----ttttgtaggctgcacctgatacttttgtcc
 || ||||||||||| ||||||||||| ||||  ||||||||||||||||  |  |  |||||||| ||||| || |||||||||||||  ||| |  |||||  |   |||     |   | ||||  ||  | |     || | |     ||  || | ||   |||||    |||| |||                      
GGGACAAAACTTTGCGAAGATGTTTGAGATCAACTTTGAGAATGAGAAAGCAGAGACAGAAATGGTGTGGCAGAATTCTTGGGCCTACAGTACCAGGACGgtaaat---acttggaagtacttagat-tatttttctcatgtgctctacaactgttaacttatcattttcaaaccttttatag----------------------
















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|7031274|gb|AW461012.1|AW461012
EST:     GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|62525869|gb|DN828517.1|DN828517
EST:     GGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|26559243|gb|CA831478.1|CA831478
EST:     GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|91052462|gb|EB162880.1|EB162880
EST:     GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|60338824|gb|DN205797.1|DN205797
EST:     GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|22521630|gb|BU080441.1|BU080441
EST:     GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|60357064|gb|DN224037.1|DN224037
EST:     GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|31359187|gb|CD443544.1|CD443544
EST:     GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGGGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|67020078|gb|CO448827.1|CO448827
EST:     GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|32935632|gb|CF040444.1|CF040444
EST:     GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|50325823|gb|CO520949.1|CO520949
EST:     GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|67027210|gb|CO455959.1|CO455959
EST:     GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|32942240|gb|CF047059.1|CF047059
EST:     GGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|51871150|gb|CV126034.1|CV126034
EST:     GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|60346669|gb|DN213642.1|DN213642
EST:     GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|87155487|gb|DY400276.1|DY400276
EST:     GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
EST: gi|32942346|gb|CF047165.1|CF047165
EST:     GGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCG                         ATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA
genomic: GGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCA

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: 476

TGGTCAAAACTTTGCCAAGATGTTTGATATCACTTTTGAGAATGAGAAAGGTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCACCAAAGGTGGCGCCAATCCAGGTAATTGTGATTCCAGTGCCTTATAAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 512

TGGTCAAAACTTTGCCAAGATGTTTGATATCACTTTTGAGAATGAGAAAGGTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCACCAAAGGTGGCGCCAATCCAGGTAATTGTGATTCCAGTGCCTTATAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 556

TGGTCAAAACTTTGCCAAGATGTTTGATATCACTTTTGAGAATGAGAAAGGTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCACCAAAGGTGGCGCCAATCCAGGTAATTGTGATTCCAGTGCCTTATAAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 386

TGGTCAAAACTTTGCCAAGATGTTTGATATCACTTTTGAGAATGAGAAAGGTGTTAGGGAAATGGTTTGGCAAAACTCTTGGGCCTACACAACCCGCTCGgtacttctca ... acccttgcagATTGGAGTGATGGTGATGACACATGGTGATGACAAAGGCTTAGTATTACCACCAAAGGTGGCGCCAATCCAGGTAATTGTGATTCCAGTGCCTTATAAGG