Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtggcatccatctgatctggtcttaattgttgtcctcgcctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACACGCTGTGGCAGATGGTCGAGATGCACGAGTGCGTCCCCGGGAAGCGTTTC

Basic information

species Zea mays
transcript GRMZM2G175321_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175321_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g14100.1 (Oryza sativa), 3'ss of exon 1
gtacgtggcatccatctgatctggtcttaattgttgtcctcgcctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACACGCTGTGGCAGATGGTCGAGATGCACGAGTGCGTCCCCGGGAAGCGTTTC
                                                               || | |   || |||   || |  |      ||||||| | |  ||   |  |  ||||||      | |||  |||  |               || |||||||| || ||||  || ||| || |||| ||||||||||| ||||||||||||||||||||||| ||||||||||||||||| || |||  ||| |||
---------------------------------------------------------------gtacata--attcattcatcatttctccttctccatttcatt--tcatcg--tccatggat------gagtgttcgattttgtttttttt-----tgtagGGGTCCGGGGGTGGCGGCGATGATCATGTCGTGGGTGATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGTGCGTGCCGGGGCGGCGGTTC

upper sequence: GRMZM2G175321_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G37340.1 (Glycine max), 3'ss of exon 1
gtacgtggcatccatctgatctggtcttaattgttgtcctcgcctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacga-actaacacaccgcatgcgtg-cagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACACGCTGTGGCAGATGGTCGAGATGCACGAGTGCGTCCCCGGGAAGCGTTTC
                                                             | |   | || ||   | | || |     |   ||||||| | |  |  || ||   |   |  ||  |   | | |   | || ||      |    |   |||||| ||||      ||   |  || |||| ||||| |||||||| ||||| |||||||| ||||| |||||||||||    || ||||| ||  | || 
------------------------------------------------------------ttcggatcatgaattactttttcttaaaccttcttccatttgatt--ttaattga---acatacttgtgtttctaatcattattatcatcatttaaaaataatagGGGTGCCGGTTCCACCGTGCTTATCTTGTCATGGGTAATCACCCTCTACACCCTGTGGCAAATGGTTGAGATGCACGAAATGGTGCCCGGAAAAAGATTT

upper sequence: GRMZM2G175321_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S5_176V6.1 (Physcomitrella patens), 3'ss of exon 2
gtacgtggcatccatctgatctggtcttaattgttgtcctcgcctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACACGCTGTGGCAGATGGTCGAGATGCACGAGTGCGTCCCCGGGAAGCGTTTC
                                                  |  | |     |   |  |||  |  ||| ||| ||    ||   |  ||| |    | |  |  |       |  |||   || |||| | |  |    | |||    ||||||| || || ||||| |   ||||  |||| ||| ||||||| ||||||||||| ||||||||||| || |||||||||   |||   ||||||||||||
--------------------------------------------------gtgagggctcctcacgttttgtcta-atccgtc-tcagagtcacacagtttcat--gttgcagtttgcggcagtgggcacaagt-aacggaatggctattcacat----gcagGGGACCGGGAGTGGTGGTGCTGGTGGTGTCGTGGATGATCACGCTGTACACGCTCTGGCAGATGGTGGAAATGCACGAGATGGTCGAGGGGAAGCGTTTC

upper sequence: GRMZM2G175321_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ10950 (Selaginella moellendorffii), 3'ss of exon 2
gtacgtggcatccatctgatctggtcttaattgttgtcctcgcctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACACGCTGTGGCAGATGGTCGAGATGCACGAGTGCGTCCCCGGGAAGCGTTTC
                                                     |  | |  | |||  | ||  |||    ||         | ||||| |   |||   |||| | |     | | |    |  |    |   |          |  | |||||| || || ||  | |   | || ||||| ||||||||||| || |||||||||||||| ||||| || ||||||||    ||||| |||||| | || 
-----------------------------------------------------acccta-gtcgtgtgtcgcccgcaatcctc-------cagctccatgttcttgacaaatggttttccaacttttc-caagcaactttaaagatttttttttcgt-tccagGGGACCGGGGGTCCTTGTTCTTGTACTGTCGTGGGTGATCACACTCTACACGCTGTGGCAAATGGTGGAAATGCACGAAATGGTCCCGGGGAAGAGATTT

upper sequence: GRMZM2G175321_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ25874 (Selaginella moellendorffii), 3'ss of exon 2
gtacgtggcatccatctgatctggtcttaattgttgtcctcgcctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACACGCTGTGGCAGATGGTCGAGATGCACGAGTGCGTCCCCGGGAAGCGTTTC
                                                              |||  |  |||  | ||          |  |  |||| |   |||   || | | |     | | |    |  |    |   |          |  | |||||| || || ||  | |   | || || || ||||||||||| || |||||||||||||| ||||| || ||||||||    ||||| |||||| | || 
-------------------------------------------------------------gtgtcacccgcaatcctcaagaactttcacagccccatgttcttgacaaatcgttttccaacttttc-caagcaactttaaagatttgtttttcgt-tccagGGGACCAGGGGTCCTGGTTCTTGTACTCTCGTGGGTGATCACACTCTACACGCTGTGGCAAATGGTGGAAATGCACGAAATGGTCCCGGGGAAGAGATTT

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|211471200|gb|FL264979.1|FL264979
EST:     GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTG                         GGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
genomic: GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
EST: gi|211471202|gb|FL264981.1|FL264981
EST:     GTCGG-TCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTG                         GGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
genomic: GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
EST: gi|149010013|gb|EE041826.2|EE041826
EST:     GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTG                         GGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
genomic: GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
EST: gi|211471201|gb|FL264980.1|FL264980
EST:     GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTG                         GGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
genomic: GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
EST: gi|211471204|gb|FL264983.1|FL264983
EST:     GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTG                         GGGTCCCGGCGTGGTCGC-ATGGTCCTGTCTTGGGTGATCACCCTGTACAC
genomic: GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
EST: gi|211471203|gb|FL264982.1|FL264982
EST:     GTCGG-TCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTG                         GGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
genomic: GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC
EST: gi|211471199|gb|FL264978.1|FL264978
EST:     GTCGGT-CCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTG                         GGGTCCCGGCGTGGTCGC-ATGGTCCTGTCTTGGGTGATCACCCTGTACAC
genomic: GTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACAC

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: 9 (upstream exon), 41 (downstream exon)
Score: 1

CCAGGAACGCCAAATGGTGGTACTCCGCCTTCCACAACGTCACGGCCATGGTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACACGCTGTGGCAGATGGTCGAGATGCACGAGTGCGTCCCCGGGAAGCGTTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 246

CCAGGAACGCCAAATGGTGGTACTCCGCCTTCCACAACGTCACGGCCATGGTCGGCGCCGGCGTCCTCAGCCTGCCCTACGCAATGTCCGAGCTCGGCTGgtacgtggca ... atgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACACGCTGTGGCAGATGGTCGAGATGCACGAGTGCGTCCCCGGGAAGCGTTTC




<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatggatatatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACACGCTGTGGCAGATGGTCGAGATGCACGAGTGCGTCCCCGGGAAGCGTTTC
                               aactaac  putative branch site (score: 246)
      atatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtggcatccatctgatctggtcttaattgttgtcctcgcctcgatcggcatgcaatattgtgccttgcatgcatctgtcgtcgcgatcgatccatttaactgatcgatggatatatggatctgcatgcgtgaacgaactaacacaccgcatgcgtgcagGGGTCCCGGCGTGGTCGCCATGGTCCTGTCTTGGGTGATCACCCTGTACACGCTGTGGCAGATGGTCGAGATGCACGAGTGCGTCCCCGGGAAGCGTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG