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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG

Basic information

species Zea mays
transcript GRMZM2G111477_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 13
gtgagattactgacctttgtatgtttactaatggcagattccatgtt-tcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattt---tgtgc-ctgtgcctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
                                   | |  | ||| | |  |  ||     ||   ||| | | ||   |   ||| |        || |  |||  |   | |||    || |   |     |||| || ||||| || ||||| |||||||||||||||||||||||||||||||||||| ||||||| |||||||||||||| |||||||||||||||||||
-----------------------------------acacacaatgatgttgagaatggaagttgaattgcactgctaggagtggtgccctgaagttatattttgacctgtatatgcatcatgacctttcctacagATCGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCATTGAATGCCACTAAAGCTGCTGTGGAAGAGGGTATTGTACCAG

upper sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 13
gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcct--cctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
                  |||||  ||||  || ||       || ||  ||   ||| |  ||| || || |      ||       || || || | |   | ||      |    ||  |||||   ||||||| ||||| || ||||| ||||||||||||||||||||||||||||| |||||| | ||||| ||||| |||||||| || ||||| || || || |
------------------gtatgcctacttgtgtca----ttttggtt--aatggtttatccctggtg-aacat-----cccactgaggttctgcaatggaaaaattgacatttaaaactgcccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG

upper sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 13
gtgagattactgacctttgtatgtttactaatggcagattccat-gtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctttcct--agATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
                                ||| | | |    | |    |||  | |  ||  | || | ||   | ||||||   || || || | ||  | ||      ||   || |  | ||  ||||||| ||||| || ||||| |||||||||||||||||||||||||||||||||||  | ||||| ||||| |||||||| || || || |||||| |||
-----------------------------gggggccgctacggccgctattgacaactatgatccctggtga-ac--atccctgtggg-gttctgcaatggcaaaattaacatttgaaactgcccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG

upper sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 13
gtgagattactgacctttgtatgtttactaatggcagatt-ccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtg-cctc-ctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
                      ||||  | ||   || || || || ||     |||    || | |  |   |||    ||| ||   ||  |    |     |  |     |||   |||| ||||   ||||||| ||||| || || || |||||||||||||||||||||||||||||||||||  | ||||| || || || ||||| || ||||| || ||||| |
----------------------gtttgtttatttgagtttaccttgctt--gctattaggattttatc-tggcacttcatcctatg---gttttgtcatgataaaactaacatctgaaacctcacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG

upper sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 13
gtgagattactgacctttgtatgtttactaatggcagatt-ccatgttt-caaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtg--cctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
                      ||||  | ||   || || || || || |    |  | || |||| ||        | |  ||  | |||| |          | ||     |||    | | ||||   ||||||| ||||| || || || |||||||||||||||||||||||||||||||||||  | ||||| || || || ||||| || ||||| || |||||||
----------------------gtttgtttatttgagtttaccttgcttgctgttaagtcttatctggtg---cttcatcatatggttttgtcatg-----ataaaattaacatctgaaaccttacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCAG

upper sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
                               |     |  || | ||   |||||     |  |    || || ||     |  || | |     || |   ||||       || |      ||  |||||||| ||||| || ||  |||||||| |||| ||||| |||||||| || ||||| || ||||| |||||||| || || || ||||||||||| ||||
------------------------------gtaatgtacacc-tcttgtgaacatcagactaataggctattaatgcattattagtttattactaatgtcgagattactcatatggg------tttttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG

upper sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
                      |||     |||  | |    ||||||      | ||       | | |     |||    ||||||       | ||   ||  |  |   ||||  |        ||||||| ||||| || ||||| ||||||||||||||||| || ||||||||||||||  ||||||| |||||||| || ||||||||||||||| ||||||
----------------------gttagtccatgttata----atgttttgggagtcttagaatcatagcagcctggttgtaagtgtcttgttataacttctggagctaat---tgtgttt--------agATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG

upper sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 13
-------------gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcc---tccatttgctgattttgtgcctgtgcctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
                | ||  |  || ||  | | |   ||  | | ||  || |   |    |  |  | |    ||  | | | |  |         | ||    |  || |    ||  ||      ||| ||| ||   |||| || |||||||| ||||| |||||| |||||||||| ||||| || |||||||| || ||||||||||| || ||||| ||||| || ||||||||||
gtctgtatcaatttacaaatccccaacattactgtctaggcttgttg-aggctctaaactcaggagctactgtactggtactcagattcatggggaatgttatctagatatatataaaaatggtggaaaattgcttccctttgcagATAGGAGGAGCTAGTGAAGCTGAAGTTAGTGAGAAGAAAGATAGGGTTACAGATGCTCTAAATGCTACTAAGGCAGCTGTAGAAGAAGGAATTGTACCAG

upper sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 13
gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtg-cctgtgcctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
                 |     |  |      ||   |||   ||| ||     | | |     ||| |    ||  |    || |  |   | || || ||  ||||   | | |        |   |||| || ||||| |||||||  || ||  |||| ||||| ||| | || || ||||||||||||||||||||||||||||| || ||||| |||||||| |
----------------gtaaggatccatctgaagcctgttcatcgttccag----tctatgatcattggagatatggcattcctg-caattaccgatgtgttgggtttgaaacttatatgattcatttcagATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACTGATGCACTGAATGCTACTAAAGCTGCTGTCGAGGAGGGGATTGTACCTG

upper sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 12
gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctt--tcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
               | |  ||||     |||      |  ||| |       ||   ||| |   || | |       ||||  ||  |  |   || | |||  |||    ||    |   |  | |||||| || |||||||| ||||  || ||    |||||||| ||  | || || |||||| |||| || ||||||||||||||||| ||||||||||| || |
------------gtatatccatgtacttcaattatctgtctcatttactcgtaatggatttgcatctgcagtttgcagtcctgattcgttattattttcgttgaaattgattttggttttttataattctagATCGGAGGAGCTAGTGAAGTCGAGGTAAACGAGAAGAAAGACCGTGTAACTGATGCATTGAACGCCACTAAAGCTGCTGTTGAGGAGGGTATTGTTCCTG

upper sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ32351 (Selaginella moellendorffii), 3'ss of exon 11
gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
                                                                       ||     |||   | || |  |      | |  | || |   |  ||   |   | |||||||| |||| ||| ||||| ||||| ||||| ||||||||| | ||||| ||||| ||||||||||| || ||||| || || ||||| || || ||||
----------------------------------------------------------------------gtatgtacaccaaagacttttgtggcagcgtttttattattgtttcgcgcgcgagcgtagATTGGAGGAGGTAGTGAAGCGGAAGTCGGTGAAAAGAAGGATCGGGTGACCGATGCGCTGAATGCTACAAAGGCTGCAGTGGAGGAGGGAATCGTGCCAG

upper sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ20894 (Selaginella moellendorffii), 3'ss of exon 11
gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
                                                                       |||     ||   | || |  |      | |  | || |   |  ||   |     |||||||| |||| ||| ||||| |||||  |||| ||||||||| | ||||| ||||| ||||||||||| || ||||| || || ||||| || || ||||
----------------------------------------------------------------------gtacgtacgccaaagacttttgtggcagcgtttttattattgtttcgcgcgcgagtgtagATTGGAGGAGGTAGTGAAGCGGAAGTCAGTGAAAAGAAGGATCGGGTGACGGATGCGCTGAATGCTACAAAGGCTGCAGTGGAGGAGGGAATCGTGCCAG

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), 48 (downstream exon)
Score: 431

GTTGATTAGATCAGCAATTGAGAATAGCACTTCAGATTATGATAAGGAAAAGCTCCAGGAGCGGTTGGCAAAACTCTCTGGAGGTGTTGCTGTTCTGAAGgtgagattac ... cctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 230

GTTGATTAGATCAGCAATTGAGAATAGCACTTCAGATTATGATAAGGAAAAGCTCCAGGAGCGGTTGGCAAAACTCTCTGGAGGTGTTGCTGTTCTGAAGgtgagattac ... cctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 326

GTTGATTAGATCAGCAATTGAGAATAGCACTTCAGATTATGATAAGGAAAAGCTCCAGGAGCGGTTGGCAAAACTCTCTGGAGGTGTTGCTGTTCTGAAGgtgagattac ... cctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 290

GTTGATTAGATCAGCAATTGAGAATAGCACTTCAGATTATGATAAGGAAAAGCTCCAGGAGCGGTTGGCAAAACTCTCTGGAGGTGTTGCTGTTCTGAAGgtgagattac ... cctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
                       tgctgat  putative branch site (score: 290)
                                    cctgtgcctcctttcc  putative PPT
                          tgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG