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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaacttcccactgcaatacaagttacagaaccctatgaaattggaaactatatttgtgatcatgacaagtgattcaccaaacagaaaatggcaaacaaatgctggactgaaaaaaaacattcctttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT

Basic information

species Zea mays
transcript GRMZM2G001895_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 21
gtgagtaacttcccactgcaatacaagttacagaaccctatgaaattggaaactatatttgtgatcatgacaagtgatt-caccaaacagaaaatggcaaacaaatgctggactgaaaaaaaacattcctttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT
|| |||||||| |   ||   |      |   ||   ||  | | ||   |     | ||| |||||| | |||| |   ||| |||  |||||||   |  | | |   || | ||| || | ||   || ||   |||||||||||||||||||| ||||||||||||||  | ||||| |||||||||||||| ||||||||||||||| |||| |||||||||||||||||||| |
gtaagtaacttactgatgagttcatccatctcgagtactccgtagttcatattcgaagttgggatcattagaagtaacagcactaaat-gaaaatgagcactagacgt--gagtaaaataaca-atgtgttctttcttagGTATGGAGTGCTTACAAGGACCAGAAGCACGATTTATTCCTCCCATCCAATGCACAGTCTTCTGCTGCTGGAGTTGCAGGGCTCATTGAGAGCTCATCGT

upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA17G12950.1 (Glycine max), 3'ss of exon 22
--------------------gtgagtaacttcccactgcaatacaagttacagaaccctatgaaattggaaactatatttgtgatcatgacaagtgattcaccaaacagaaaatggcaaacaaatgctggactgaaaaaaaacattcctttttatgt---agGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT
                       |||||  |  ||  |   | | ||||   |     ||     |||| | || | |     ||  ||     |  |    |||  | | |     ||     |  |    |  | ||  |  |||| |  || ||   |||| |||||||||||||||||||||||||| || || ||||| || || ||||| |||||| | |||||||| |||||||| ||||||||||  |||||||
gtaagtctcaacacatgtagagtagtaatatggcatggttgttcgagtttttggcttttacctc-ttggcacctctgtgc---attttgctgcatcctgttgcaagtatacatatctaagt---ttttaccttctacaatcattttccctcctacgttccagGTTTGGAGTGCTTACAAAGACCAGAAGCATGATCTCTTCCTCCCTTCAAATGCTCAATCTGCAGCTGCTGGCATTGCTGGTCTCATTGAGAATTCATCAT

upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA05G08040.2 (Glycine max), 3'ss of exon 22
---------gtgagtaacttcccactgcaatacaagttacagaaccctatgaaattggaaactatatttgtgatcatgacaagtgatt-caccaaacagaaaatg-gcaaacaaatgctggactgaaaaaaaacattcctttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT
            ||||| ||  ||  ||  |   ||||   |   | |  |    | |  |||  |  |||| |     |   || || || |     |  | |   | | | |   ||    |          |   ||   | |  |||| |||||||||||||||||||||| ||| || || ||||| || || ||||| |||||| | |||||||| |||||||| ||||||||||  |||||||
gtaagtctcaacagtaatttaacatggctgtttgagttgttgg--ctttagcctcttggcacttcagatgtggtttctgcttttgtttgcatcctgttgctagtatactatccatatctaagttttctccttctacaactgcgt-tccagGTTTGGAGTGCTTACAAAGACCAGAGGCATGATCTCTTCCTCCCTTCAAATGCTCAATCTGCAGCTGCTGGCATTGCTGGTCTCATTGAGAATTCATCAT

upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 21
gtgagtaacttcccactgcaatacaagttacagaaccctatga-aattggaaactatatttgtgatcatgacaagtgattcaccaaacagaaaatggcaaacaaatgctggactgaaaaaaaacattcctttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT
                        || |  |   ||  | ||| || ||||   |  | |  ||||| |   ||   |    ||   || ||| | |  | ||||| |   |           | || ||   | || |||| |||||||| || |||||||||||||| || || |||||||| || ||||| |||||| ||||||||||||||||||| || |||||||  |||||||
----------------------gaaaatcccg--actttgtgacaagtggaggttgaagtgctgatcttttgaa---acctgcc---caaaaatttgtgaccaaattcctcat----------ctttgctggatttgcagGTTTGGAGTGCCTATAAAGACCAGAAGCATGATCTATTCCTTCCTTCTAATGCTCAATCTGCTGCTGCTGGAATTGCTGGTCTTATTGAGAATTCATCAT

upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 15
lower sequence: PP1S60_221V6.1 (Physcomitrella patens), 3'ss of exon 21
-------------------gtgagtaacttcccactgcaatacaagttacagaacccta------tgaaattggaaactatatttgtgatcatga-caagtgattcaccaaacagaaaatggcaaacaaat-gctgga-ctgaaaaaaaacattcctttttatg-----tagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT
                    ||  ||  ||       || | | ||     | ||| ||       |||| |  ||| | |  || |  ||  |  || ||||    |          |||        || | || | |||   | |||       |||          ||||||||||||||||||| || ||||||||||| || ||| | || || ||||| ||| || | || ||||| || ||||| || ||||| | ||| ||  
gtacgatctctttctatctctgtctaggttttgctaacatttcgagcatgggcaccttaagcattcgaaactaaaaagtgtcgttctactctggttcaggtgacgtgcttgttgttttatgattgttggattgttgaaactgttgacaaatgagttgtttcggaattatcagGTATGGAGTGCTTACAAGGATCAGAAGCACGATCTCTTCTTACCTTCAAATGCCCAAACTGCCGCAGCTGGTATAGCTGGTCTTATTGAAAACTCCTCTG

upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 15
lower sequence: EFJ35138 (Selaginella moellendorffii), 3'ss of exon 22
gtgagtaacttcccactgcaatacaagttacagaaccctatgaaattggaaactatatttgtgatcatgacaagtgattcaccaaacagaaaatggcaaacaaatgctggactgaaaaaaaacattcctttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTC-ATCAT
                                                                  |||| |     ||         |     |     |  |   |    |  ||    || ||||         |||| |||| ||| ||||||||||||||||||||| | ||||| ||||| ||  | ||     | || |||||||| ||||| || || ||  |||| | |  
----------------------------------------------------------------gtatgagagacactttcttcgttggtcttcgttgtcctcacctt---ttccaactccacgttcc---------agGTGTGGAATGCATACAAAGACCAGAAGCACGACTTGTTCCTGCCATCAAACTCTCAGATGGCCGCGGCTGGAATAGCTGGCCTGATCGAAGGCTCCACCG-

upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 15
lower sequence: EFJ24089 (Selaginella moellendorffii), 3'ss of exon 22
gtgagtaacttcccactgcaatacaagttacagaaccctatgaaattggaaactatatttgtgatcatgacaagtgattcaccaaacagaaaatggcaaacaaatgctggactgaaaaaaaacattcctttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTC-ATCAT
                                                                  |||| |     ||         |     |     |  |   |    || ||    || ||||         |||| |||| ||| ||||||||||||||||||||||| ||||| ||||| ||  | |||    | || |||||||| || || || || ||  |||| | |  
----------------------------------------------------------------gtatgagagacactttcttcgttggtcttcgttgtcctcacctt---ttgcaactccacgttcc---------agGTGTGGAATGCATACAAAGACCAGAAGCACGACCTGTTCCTGCCATCAAACTCTCAAATGGCCGCGGCTGGAATAGCGGGCCTGATCGAAGGCTCCACCG-

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|109637212|gb|EC590757.1|EC590757
EST:     CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGAT                         GTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
genomic: CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
EST: gi|16927351|gb|BM080420.1|BM080420
EST:     CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGAT                         GTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
genomic: CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
EST: gi|6012267|gb|AW061809.1|AW061809
EST:     CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGAT                         GTATGGAGTGCTTACAAAGACCAGAAGCACGACCT
genomic: CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCT
EST: gi|5919503|gb|AW054600.1|AW054600
EST:     AGAGTTCGTGAAGTCCTGAATTCCTCTGAT                         GTATGGAGTGCTTACAAAGACCAGAAGCNCGACCTTTTCCTTCCATCCAAT
genomic: AGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
EST: gi|71596430|gb|DR907181.1|DR907181
EST:     CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGAT                         GTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
genomic: CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
EST: gi|32919339|gb|CF024151.1|CF024151
EST:     TGAATTCCTCTGAT                         GTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
genomic: TGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
EST: gi|89761888|gb|DY689721.1|DY689721
EST:     CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGAT                         GTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT
genomic: CCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAAT

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), 45 (downstream exon)
Score: 178

GTGCTTCATGCTTTTGCAACCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 127

GTGCTTCATGCTTTTGCAACCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 303

GTGCTTCATGCTTTTGCAACCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 250

GTGCTTCATGCTTTTGCAACCGAAGGTGCACATTGTGCTAGAGTTCGTGAAGTCCTGAATTCCTCTGATgtgagtaact ... ttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacagaaaatggcaaacaaatgctggactgaaaaaaaacattcctttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT
                                      cattccttttt  CT-rich tract
                              aaaaaaaacattcctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaacttcccactgcaatacaagttacagaaccctatgaaattggaaactatatttgtgatcatgacaagtgattcaccaaacagaaaatggcaaacaaatgctggactgaaaaaaaacattcctttttatgtagGTATGGAGTGCTTACAAAGACCAGAAGCACGACCTTTTCCTTCCATCCAATGCACAATCTTCTGCTGCTGGAATTGCTGGGCTCATTGAGAGCTCATCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA