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'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACCGTCGCTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgtttttgtaaaccatgtgatcttctgaatgaaacttactggatttcttttacagagcttgatcagttttatcactgcttggttgtttttatgtgagagtgtgccatgatcttgtttctgttccttttgtatgtacag

Basic information

species Zea mays
transcript GRMZM2G028096_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028096_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g39300.1 (Oryza sativa), 5'ss of exon 10
TGACCGTCGCTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgtttttgtaaaccatgtgatcttctgaatgaaacttactggatttcttttacagagcttgatcagttttatcactgcttggttgtttttat-gtgagagtgtgccatgatcttgtttctgttccttttgtatgtacag
|||||| || |||||||||||||||||||||||||||||||||||||||||||| ||||||||||  || || |||||||||||  | ||||   ||   |||| | || |||||| | || | |              | | |  ||  |||  |  |  || |  || |    |  ||  || ||| | |                                
TGACCGGCGTTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAGgtgaggtttttcgaaat-tgtgctattttgaatggagctaagt--------ccggtggggttgcat--gttagacaagggcctttttatgggaacagtaggattgtcctac-------------------------------

upper sequence: GRMZM2G028096_T03 (Zea mays), 5'ss of exon 11
lower sequence: Vv04s0023g00800.t01 (Vitis vinifera), 5'ss of exon 10
TGACCGTCGCTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgtttttgtaaaccatgtgatcttctgaatgaaacttactggatttcttttacagagcttgatcagttttatcactgcttggttgtttttatgtgagagtgtgccatgatcttgtttctgttccttttgtatgtacag
|||||||||||| ||||||||||||||||| || |||||| |||| |||||||  || ||||| |   || | || || |||||  | |    | |     |||||| | |    | | || | |   | | ||||     |     |  ||| |||  |   ||||     ||  |   | |  |    || || |                          
TGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATATGCAAATCCGTGAAAAGCTGGCAGAGCTTCAGgtaagatga-attattttcgtgatcatata---ggagctcatt---tatgttttg-gttgtcccgtgggttctatttcatattgg---cattagtacaaaaagg----ataattt--------------------------

upper sequence: GRMZM2G028096_T03 (Zea mays), 5'ss of exon 11
lower sequence: PP1S88_36V6.2 (Physcomitrella patens), 5'ss of exon 10
TGACCGTCGCTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgtttttg-taaaccatgtgatcttctgaatgaaacttactggatttcttttacagagcttgatcagttttatcactgcttggttgtttttatgtgagagtgtgccatgatcttgtttctgttccttttgtatgtacag
|||||||||| |||| || |||||||||||||| || ||| ||||||| ||||  || || ||||   |   |||  |||  ||  || ||   |  ||| | |||  || |   || ||   |  | |||   | |  |  | ||  ||  |  | |||| | ||||     |   || |   |||                                     
TGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACATGCAGATTCGGGAGAAGCTTGTTGACTTGCGAgtacgtcttcaattcaccttctgagatt-tatttggaaagaatggtattgtgtgtgtattgtttcttc--tagtgtcacagattgga-acatcagtgcg---gtgca-----------------------------------

upper sequence: GRMZM2G028096_T03 (Zea mays), 5'ss of exon 11
lower sequence: PP1S402_41V6.1 (Physcomitrella patens), 5'ss of exon 10
TGACCGTCGCTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgtttttgtaaaccatgtgatcttctgaatgaaacttactggatttcttttacagagcttgatcagttttat-cactgcttggttgtttt-tatgtgagagtgtgccatgatcttgtttctgttccttttgtatgtacag
||||||||||||||| || |||||||||||||| || ||| ||||||||||||  || |||||||   |   |||  ||| |||  |   || |      |   |  |||  |            |  ||| ||||  | ||| || | |      |  | ||| |||| ||     |  |  || | | | | |   | |                        
TGACCGTCGCTTGGCGGACCATTTTGGAGGGAAGCTGCATTTGGGTTATATGCAGATTCGTGAGAAGCTCGTTGACTTGCGGgtacgcgcttat------ttctactttccaa------------gattttgttttcaaaagcatggtaaagcgcgtgtattgcctggtagtgccacaaataggaatat-ctaagtggtgg------------------------

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|50324674|gb|CO519800.1|CO519800
EST:     AACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAG                         GAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG
genomic: AACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgttttt ... gtatgtacagGAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG
EST: gi|60357771|gb|DN224744.1|DN224744
EST:     AACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAG                         GAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG
genomic: AACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgttttt ... gtatgtacagGAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG
EST: gi|18174490|gb|BM349878.1|BM349878
EST:     AACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAG                         GAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG
genomic: AACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgttttt ... gtatgtacagGAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG
EST: gi|166555935|gb|EG131352.1|EG131352
EST:     AACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAG                         GAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGC
genomic: AACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgttttt ... gtatgtacagGAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGC
EST: gi|18164732|gb|BM334571.1|BM334571
EST:     ACTTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAG                         GAATAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG
genomic: AC-TTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgttttt ... gtatgtacagGAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG
EST: gi|18167102|gb|BM336941.1|BM336941
EST:     AACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAG                         GAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG
genomic: AACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgttttt ... gtatgtacagGAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG
EST: gi|18168036|gb|BM337876.1|BM337876
EST:     AACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAG                         GAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG
genomic: AACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgttttt ... gtatgtacagGAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG
EST: gi|5566994|gb|AI881905.1|AI881905
EST:     AACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAG                         GAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG
genomic: AACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgttttt ... gtatgtacagGAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG

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 2 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 23 (downstream exon)
Score: 3

TGACCGTCGCTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgttttt ... gtatgtacagGAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG


Block sizes: 49 (upstream exon), 23 (downstream exon)
Score: 7

TGACCGTCGCTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgttttt ... gtatgtacagGAAGAGAAGAACAAAAAACGGAAGCTAGACCGAGCTGAGTATGACAGAAG




<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACCGTCGCTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAGgtttgtttttgtaaaccatgtgatcttctgaatgaaacttactggatttcttttacagagcttgatcagttttatcactgcttggttgtttttatgtgagagtgtgccatgatcttgtttctgttccttttgtatgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG