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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattttagggagccctcttttactttagtcaacctatttatcgagcttcactttctttttgtttaacaatatatcaatatatgccttgatggaatgaactgtccccaagggaaatacgttggttttttcctaatatagatcactttatttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG

Basic information

species Zea mays
transcript GRMZM2G043056_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g11820.1 (Oryza sativa), 3'ss of exon 3
gtaagtattttagggagccctcttttactttagtcaacctatttatcgagcttcactttctttttgtttaacaatatatcaatatatgccttgatggaatgaactgtccccaagggaaatacgttggtttt-ttcctaatatagatcactttatttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG
|||||  | |||   ||  || ||||  |  | |      || | |||| | || ||  |||         || | |  |    | ||     ||   ||| | | |    |||  |   |   |  |||| ||  | | | |  |   |||  ||  |||| || ||||| || |||||||  || || ||||| ||||| |||||||| ||||| ||||||  ||||||||||||||| || ||||||
gtaagattcttattcagttctgttttgttacacttg--taatatgtcgaacctctctagctt---------cactgtccc----tttggtcaaattagatgcattttagtgaagtcagtgatcctaattttattgatgacaaaatttgttttgctt--ctagCCGAGAGTTCACGCATCGAGCGAAGTCAGTTTCTATGGCTAAATTTACTGCACAGGAAGTTAGTGCCCTTCAAGAAGGAGGAAATGAG

upper sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G09750.2 (Glycine max), 3'ss of exon 3
gtaagtattttagggagccctcttttactttagtcaacctatttatcgagcttcactttctttttgtttaacaatatatcaatat-atgccttgatggaatgaactgtccccaagggaaatacgttggttttttcctaatatagatcactttatttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG
                                                   ||   ||      | ||  |  ||| |  ||||| ||  |||  | |  |  ||| | ||    | |   | ||    |  ||  |  | |             ||| ||||||||| || || |||||||||||||| ||||| ||||| || |||||  |||||||||||  ||| ||||||||||| || ||| ||
------------------------------------------------cattttgtttaaaaaatattgga-gatagaataatatcatttctttctagtgttcacttttcctt--gaatgaaagtcaactgctttttgttttga-----------tttatagTCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCACTTCAAGAAGGAGGCAATCAG

upper sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G29960.1 (Glycine max), 3'ss of exon 1
gtaagtattttagggagccctcttttactttagtcaacctatttatcgagcttcactttctttttgtttaacaatatatcaatatatgccttgatggaatgaactgtccccaagggaaatacgttggttttttcctaatatagatcactttatttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG
                                                      | ||        |||||  |||||| | |  ||   |  ||       | ||| |       | |  | ||  | | | | |||| |  ||   ||     ||  || || |||||||||||| ||||||||||||| || ||||| |||||| |  || |||||||  |||| ||||||| ||| || ||||||
------------------------------------------------------atttaagccaattttaattatatattatttgatatttatattttcatcattgttc-------atagtcatttttatgtacttaatttccatgttttatgaattacagCCGAGAGTTTACACATAGAGTAAAATCTGTGTCAATGGCTAAATTTTCTCCAGAAGAAGTCACTGCTCTTCAAGCAGGTGGCAATGAG

upper sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G32050.1 (Glycine max), 3'ss of exon 1
gtaagtattttagggagccctcttttactttagtcaacctatttatcgagcttcactttctttttgtttaacaatatatcaatatatgccttgatggaatgaactgtccccaagggaaatacgttggttttttcctaatatagatcactttatttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG
                                             |  |  |  | | |  | |    ||   ||| |  ||||  |   |   |  | ||  |  |   | | | || |    || |||||      | | |||          || ||| ||||| || || |||||||||||||| ||||| ||||| || |||||  |||||||||||  ||||||||||||||| |||||| ||
--------------------------------------------tttaaaatatattgtgctgta--ctagagataaaataataactttttatttctagtgtccacttttctatgaaagtcaactgtttttt-----gtgttgat----------ttatagCCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCCCTTCAAGAAGGAGGGAATCAG

upper sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G35310.1 (Glycine max), 3'ss of exon 3
gtaagtattttagggagccctcttttactttagtcaacctatttatcgagcttcactttctttttgtttaacaatatatcaatatatgccttgatggaatgaactgtccccaagggaaatacgttggttttttcctaatatagatcactttatttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG
                                                         || |  || ||| | |||||   | | ||      ||| | |  |  |     ||   ||  |  |||   ||| |||| |  |   |    ||   |||| || || |||||||||||||| |||||||| ||||| ||||| |||||||  ||||| ||||||  ||| ||||||||||| || ||| ||
--------------------------------------------------------attgtaattatttta-aatattctattgtac-tagagataggacaatgttgtttca---gacttcagtttactttctcctcaactgccttttgtttaatttccagCCGAGAGTTTACACATCGGGTAAAATCAGTTTCAATGGCTAAATTTAGTGCACAGGAAGTTAGTGCACTTCAAGAAGGAGGAAATCAG

upper sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G04420.2 (Glycine max), 3'ss of exon 2
gtaagtattttagggagccctcttttactttagtcaacctatttatcgagcttcactttctttttgtttaacaatatatcaatatatgccttgatggaatgaactgtccccaagggaaatacgttggttttttcctaatatagatcactttatttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG
                                                   | ||  || |  || ||| | |||||     | ||      ||| | |  |  |     ||          |||   ||| | || |  |   |    ||   |||| || || || ||||||||||| |||||||| ||||| ||||| |||||||  ||||| ||||||  ||| ||||||||||| || ||| ||
-------------------------------------------------tgtccaaattgtaattatttta-aatattctgttgtac-tagagataggacaatgttgtttca----------gtttcctttcttctcaactgccttttgtttaatttccagCCGAGAATTTACACATCGGGTAAAATCAGTTTCAATGGCTAAATTTAGTGCACAGGAAGTTAGTGCACTTCAAGAAGGAGGAAATCAG

upper sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G13350.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtattttagggagccctcttttactttagtcaacctatttatcgagcttcactttctttttgtttaacaatatatcaatatatgccttgatggaatgaactgtccccaagggaaatacgttggttttttcctaatatagatcactttatttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG
                                                                    | |   ||  | |   | |    |  | |  |  |  ||   ||  ||||||        || ||    ||||  ||   | | |||    ||||| |||||||||||||| || |||||  | || ||||| ||||||||| ||||||||||| ||||  |  ||||||| || ||| ||
-------------------------------------------------------------------gtgagtgtactttatcttctcatattcttgtgtagatggtgttcattggaaatg-------ttgtttgagatatgcatatgtatttttgaacagTCGTGAGTTTACACATCGTGTTAAATCGATATCAATGGCGAAATTTACCTCACAAGAAGTTACTGCTTTGAAAGAAGGTGGAAATCAG

upper sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0002g04860.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtattttagggagccctcttttactttagtcaacctatttatcgagcttcactttctttttgtttaacaatatatcaatatatgcct-tgatggaatgaactgtccccaagggaaatacgttggttttttcctaatatagatcactttatttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG
                                                            | ||      |   | | |  | |  ||  | || |   |   | || |   |     |||  ||  | | |  | || | |  ||  | | |   ||| ||||||||||| |||||| |||| |||||||| || ||||| ||||||||  | ||||||||| || |||||||| | ||||||||||||
------------------------------------------------------------tgttacgaggatggtgtgttgacaattgggtctgtttataaatattggctttatcaacaat-tgtgtgctctgacttattttttatttcataacaattc-agTCGGGAGTTCACACATAGAGTGAAATCTGTGTCGATGGCTAAATTTACTTCTCAAGAAGTTACTTCCCTTCAAAATGGGGGGAATGAG

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|78087088|gb|DV515481.1|DV515481
EST:     GTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA                         TCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGC
genomic: GTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACAgtaagtattt ... atttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGC
EST: gi|71428282|gb|DR809332.1|DR809332
EST:     GTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA                         TCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGC
genomic: GTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACAgtaagtattt ... atttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGC
EST: gi|211246819|gb|FL131898.1|FL131898
EST:     GTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA                         TCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGC
genomic: GTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACAgtaagtattt ... atttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGC
EST: gi|78115033|gb|DV533421.1|DV533421
EST:     GTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA                         TCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGC
genomic: GTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACAgtaagtattt ... atttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGC

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), 48 (downstream exon)
Score: 380

GGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACAgtaagtattt ... atttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

GGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACAgtaagtattt ... atttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

GGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACAgtaagtattt ... atttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 143

GGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACAgtaagtattt ... atttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccccaagggaaatacgttggttttttcctaatatagatcactttatttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG
                          tcctaat  putative branch site (score: 143)
                                      tcactttatttttct  putative PPT
                             taatatagatcacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattttagggagccctcttttactttagtcaacctatttatcgagcttcactttctttttgtttaacaatatatcaatatatgccttgatggaatgaactgtccccaagggaaatacgttggttttttcctaatatagatcactttatttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG