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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgctgaatgtgacagggttcattttgcggtcatctacttttgttcttgtttttcttttaatttgcccttacctctcctctattgtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGC

Basic information

species Zea mays
transcript GRMZM2G128877_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 4
-------gtgcgctgaatgtgacagggttcattttgcggtcatctacttttgttcttgtttttcttttaat-ttgcccttacctctcctctattgtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGC
         |   ||||||||      ||   |||    |         |||  ||  || |   || | | ||| | |  ||| |   |||| |||||||||||||||||| ||||| ||||| ||||| || ||||||||||| ||||| |||||||| |||||||||||||||||||||||||| || ||| | ||| |||
gtacttcaagttgtgaatgtggagtaatttcatttattttttaagctccttgcactccttgtctgttaactcttgtcatgtcctttttcctatcgtgtttgcagCGCCCTCTGAAAACTATTGCTATTAAATCTGGAGATGTGTACATTCCGCGTGGTGTCTCAGTTCCTGCCCTTGACAAAGATGCTTTGTGGCATTTTAAGC

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 4
--gtgcgctgaatgtga-cagggttcattttgcggtcatctacttttgttcttgtttttcttttaatttgcccttacctctcctctattgtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGC
  ||||  |     | | |||         | |  |  | | | ||| |||   | || ||| ||| ||      |    | || |||  ||    ||| | ||| | ||||| ||||| |  |  || || ||||| ||||||||||||||||| || ||||| || || ||||||||| || | ||||||||||| |
gtgtgccttttccctaatcagaacattcacttcaattcttttcctttcttcgcctcttccttctaactta-----aatatttctttatcctg---acagAGGCCTTTGAAAACTATTGCTAAAAGATCTGGTGATGTCTATATTCCTCGTGGTGTCTCTGTTCCAGCACTCGACAAAGATACACTTTGGGAATTTCAAC

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 4
gtgcgctgaatgtgacagggttcattttgcggtcatctacttttgttcttgtttttcttttaatttgcccttacctctcctctattgtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGC
||| ||    | |  |   |  ||   | |  |    | |||||  | |  |    | ||   | |  | | |    | || |||  ||    ||| | ||| | ||||| ||||| |     || || ||||| ||||||||||||||||| || ||||| || || ||||||||| || | ||||||||||| |
gtgtgcc--ttttccctaagcacaacattcacttcaattcttttcctttcttccccccttctttctaacttaaatatttctatatcctg---acagAGGCCTTTGAAAACTATTGCTAAACGATCTGGTGATGTCTATATTCCTCGTGGTGTCTCTGTTCCAGCACTCGACAAAGATACACTTTGGGAATTTCAAC

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------------------------------gtgcgctgaa----tgtgacagggttcattttgcggtcatctacttttgttcttgtttttcttttaatttgcccttacctctcctctattgtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGC
                                                                     | || ||||     ||  |  | |||  |||     ||| |   | |         |  | | | |   ||  |||     || | | |      ||||| | ||| | || |||||||| |  |  || || ||||| || |||||||||||||| || |||||||| ||||||||||||  | | |||||||| ||||
gttcgtgtaaattctgatagataaagggtctcttaagctgtttcatattgttcaactttgactttgtttgagcactgatcagctgctattgagtttctttcattttcaaccgttctgcagagcactagtatataacgatgttctttttgttcttatttaa----tgcagAGGCCTTTGAAGACCATTGCAAAAATATCTGGTGATGTCTACATTCCTCGTGGTGTATCTGTTCCTGCACTTGACAAAGATATACTCTGGGAATTCCAGC

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 4
gtgcgctgaatgtgacagggttcattt-tgcggtcatctacttttgttcttgtttttcttttaatttgcc--cttacctctcctctattgtgtt--tgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGC
 |     || |   |     ||  ||| | |        |   || |     |      |  || |  |    |||  |    ||| |||| ||  ||||| | || || || || ||||| |  |  || || ||||| |||||||||||||||||||| || || ||||||||||||||| || ||||||| || ||||
-tatatggattcccaacatttttgtttattcaaatgggcagcattataggcttccacagtagaaatctctaatttaattgctttcttttgtattaatgcagAGGCCACTGAAGACTATTGCTAAGAGATCTGGTGATGTCTATATTCCTCGTGGTGTTTCTGTCCCAGCCCTTGACAAAGATACACTATGGGAGTTCCAGC

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 4
-gtgcgctga-atgtgacagggttcattttgcggtcatctacttttgttcttgtttttct-tttaatttgcccttacctctcctctattgtgtttg-cagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGC
  |||  | | |||       ||  | ||    || |||  || |  || | ||        ||  |||| |   |  | |    ||||   ||   ||||| ||| | ||| | |||||  || |||     |||||||||||||||||||| ||| |||| ||||| ||||| | | |       ||||||||  | |
tatgcattaatatgcacatctgtctacttgaatgttatcatctctacttttagtcaagagacttcctttgacacgatatttgtggtatttccttgaacagCGGCCTTTGAAAGCTATTGCACTTCAGTGTCAGGATGTGTATATTCCTCGTGGAGTTGCAGTGCCTGCTCTTGATAGAAAGAGGCAGTGGGAATTCAAAC

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 3
gtgcgctgaatgtgacagggttcattttgcggtcatctacttttgttcttgtttttcttttaa---tttgcccttacctctcctctattgtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGC
                                           | |    | | | | |  ||   || |   | |  |||  | | ||   ||||||||| ||||| ||| |||||||||||||||| || ||||| || || || || || ||| | || || || |||||||| |||    | ||||||||    |
------------------------------------------gtatcacggctatgcatgaaaactttggttttgaggtctattttgtttgatttgcagCGTCCTCTTAAATCCATTGCCATTAAGTCGGGCGATGTCTACATCCCGCGAGGAGTTGCTGTGCCAGCACTTGACAAGGATAAGCTGTGGGAATTCTCTC

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|116813623|gb|EC856086.1|EC856086
EST:     AGTTGAACTTGGGACCTGGAA-TCTTGG-AATATTTTTGATGGTATCCAG                         CGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGT
genomic: AGTTGAA-TTGGGACCTGGAATTCTTGGAAATATTTTTGATGGTATCCAGgtgcgctgaa ... gtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGT
EST: gi|33095058|gb|CF055052.1|CF055052
EST:     CAGTTGAATTGGGACCTGGAATTCTTGGAAATATTTTTGATGGTATCCAG                         CGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGT
genomic: CAGTTGAATTGGGACCTGGAATTCTTGGAAATATTTTTGATGGTATCCAGgtgcgctgaa ... gtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGT
EST: gi|211154399|gb|FL123518.1|FL123518
EST:     CAGTTGAATTGGGACCTGGAATTCTTGGAAATATTTTTGATGGTATCCAG                         CGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGT
genomic: CAGTTGAATTGGGACCTGGAATTCTTGGAAATATTTTTGATGGTATCCAGgtgcgctgaa ... gtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGT
EST: gi|5525243|gb|AI861241.1|AI861241
EST:     CAGNTGAATTGGGACCTGGAATTCTTGGAAATATTTTTGATGGGATCCAG                         CGCCCTCTAAAAACCATTGCCATTA
genomic: CAGTTGAATTGGGACCTGGAATTCTTGGAAATATTTTTGATGGTATCCAGgtgcgctgaa ... gtgtttgcagCGCCCTCTAAAAACCATTGCCATTA
EST: gi|149014926|gb|EE044655.2|EE044655
EST:     CAGTTGAATTGGGACCTGGAATTCTTGGAAATATTTTTGATGGTATCCAG                         CGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGT
genomic: CAGTTGAATTGGGACCTGGAATTCTTGGAAATATTTTTGATGGTATCCAGgtgcgctgaa ... gtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGT

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), 49 (downstream exon)
Score: 268

CCTCTATCAGTTGAATTGGGACCTGGAATTCTTGGAAATATTTTTGATGGTATCCAGgtgcgctgaa ... gtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 458

CCTCTATCAGTTGAATTGGGACCTGGAATTCTTGGAAATATTTTTGATGGTATCCAGgtgcgctgaa ... gtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 265

CCTCTATCAGTTGAATTGGGACCTGGAATTCTTGGAAATATTTTTGATGGTATCCAGgtgcgctgaa ... gtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 536

CCTCTATCAGTTGAATTGGGACCTGGAATTCTTGGAAATATTTTTGATGGTATCCAGgtgcgctgaa ... gtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttcttgtttttcttttaatttgcccttacctctcctctattgtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGC
                          cccttac  putative branch site (score: 536)
                          cccttacctctcctct  CT-rich tract
       ttgtttttcttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgctgaatgtgacagggttcattttgcggtcatctacttttgttcttgtttttcttttaatttgcccttacctctcctctattgtgtttgcagCGCCCTCTAAAAACCATTGCCATTAAGTCAGGAGATGTGTATATTCCTCGTGGTGTTTCAGTTCCTGCCCTTGACAAAGATGCATTATGGGAATTTCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG