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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctataagcaggtcattagatgcttatataatccataagctggattatataatcttgagaggaaacaaacatggccttaatcatgcatccttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA

Basic information

species Zea mays
transcript GRMZM2G316967_T01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
atctataagcaggtcattagatgcttatataatccataagctggattatataatcttgagaggaaacaaacatggccttaatcatgcatccttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
                 || ||||| | |||     |    ||||| | ||| |         |||   |       ||||| |||| |||||| |||||||||||||||||||||||||||| || ||||||||||| ||||||||||||||||||||||||||||| ||||||||||| |||||||||||||||||||
----------------gtaaatgctca-atatctttt---ttggataa-atacttc------aaaattcaggaaattttaattatgcttccttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 21
atctataagcaggtcattagatgcttatataatccataagctggattatataatcttgagaggaaacaaacatggccttaatcatgcatcc---ttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
                         || ||  |||| |      |  ||   ||        |   |||   |  |  ||  | |   |     ||||  ||||| |||||||||||||||||||| ||||| || || || ||| |||| || ||||||||||| |||||||||||||| || || ||||| |||||||| |
------------------------gtacatg-tccagagatacaaccatgacattccatacagccgcaatgtttactgtatacttaggtttattttctatcagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 20
atctataagcaggtcattagatgcttatataatccataagctggattatataatcttgagaggaaacaaacatggccttaatcatgcatc--cttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
         || |||   |||| |   || || |          |||| ||    ||  |  |  |        |  ||| | |||  |    ||||  ||||| |||||||||||||||||||| || || || || || ||| | || || ||||||||||| || ||||||||||| || || ||||| |||||||| |
------gtacatgtccagagatacaagtacaacc----------attacattccgttccgctgctatgttttctgt-ttacttatggtttattttctatcagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAA

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
lower sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 20
----------------------------atctataagcaggtcattagatgcttatataatccataagctggattatataatcttgagaggaaacaaacatggccttaatcatgcatccttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
                                   ||||  ||  || || || |||     ||  ||||  || | |  || |    |  |  | ||  |      | |  | |  | ||| ||||||| |||||||| ||||||||||| |||||||| ||||| || || |||||||| |||||||| ||||| || || ||||| || ||||| || || |  |
gtaagcagcttaatccaactttttctgttctcgggagcatctc-ctaaatactgatac--ctcaggagcta-atgaaactatttgagtaatatgcgaagctaaatgcatttttcc--ctttcgtgcagGTAATGACAACTTTCATGCCACCGCCACCAGCTTCAACTTTCTTGGCATTTCATCCTCAAGATAATAATATTATTGCAATCGGGATGGAGGACTCGAGTA

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 20
------------------atctataagcaggtcattagatgcttatataa-----tccataagctggatta-tataatcttgagaggaaacaaacatggccttaatcatgcatccttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
                  | ||  ||  | | ||  ||||   ||  | |     | |  |  ||    || || | ||||  |      | ||  |  |   ||  |   ||    |||  |||||||||||||||||||||| ||||||||||||||||| ||||| || || || ||||| ||||||||| |||| || || ||||||||||| || || |
gtatatattatctatatgaacttaaaaaaagccacaagatttctaactgaaaatgttctcacactaatctagtaaactcttttggttgttctaatttc-cacaaaaaaactattggccttatagGTGATGACAACATTCATGCCGCCTCCACCAGCATCAACGTTTTTGGCGTTCCATCCTCAGGACAATAACGTCATCGCCATTGGAATGGAAGACTCTACGA

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
atctataagcaggtcattagatgcttatataatccataagctggattatataatcttgagaggaaacaaacatggcctta-atcatgcatccttc--ttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
                    |||  || | |   || |   | |  | | | |||      || |    | ||||  |   || |||   | |||  ||| |||| ||||||||||||||| ||||||| || || ||||| ||  |||| || || ||||||||||||||||||||||| ||||||||||| ||||| ||||
------------------gtatgtctaaaca--tcacagttttgcatct-tcatcaaatttggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 20
atctataagcaggtcattagatgcttatataatccataagctggattat--ataatcttgagaggaaacaaacatggccttaatcatgcatccttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
     |||  |  |          || ||| ||  | ||  |    |     | ||  |   |     ||    || |  |   | |       |  | ||||| ||||| ||||||||||| || || |||||| | || ||| | || || || || |||||||| |||||||| || ||||||||||| |||||||| |
--tattaaaaaaattgaagccattttttattattaaaaaattactctgctggtgatgcttgaacatggcagttctgacagttgccttcggattgtgattcagGTCATGACGACATTCATGCCGCCACCTCCAGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAA

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 20
------------atctataagcaggtcattagatgctta--tataat-------ccataagc----tggattatataatcttgagaggaaacaaacatggccttaa------tcatgcatccttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
            |   || || ||   |||  || |||   | ||||         | ||||    ||  ||   |||| |||| ||    |||   |     | |      || |      ||    ||||| ||||| |||||||||||||| || |||||| | || ||| | |||||||| || |||||||| || ||||| || || |||||||||||||| || |
gtaaagtccgcgaatcatgaggagtctattttattctttgttctaataatatggtgagaagcgttttgtttttggtaattttgacagttgtcaatttttattctgacgcttttcttcggattttgactcagGTCATGACGACATTCATGCCACCACCTCCAGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAA

upper sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
atctataagcaggtcattagatgcttatataatccataagctggattatataatcttgagaggaaacaaacatggccttaatcatgcatccttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
                                    || ||   ||| |    ||||||  ||    | |  | ||| |                | |||||||||||| ||||||||||||| ||||||||| |||| ||  | || ||||||||||||||||| || |||||||| || |||||||||||||| || |
-----------------------------------gtatgc-acatttttccttcttgaccggtgtaagaacttgccatg---------------tccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA

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|33094201|gb|CF054195.1|CF054195
EST:     TGTCTACTTGTGGTGGGAAGGTTTCTTTGTTTAACATGATGACATTCAAG                         GTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTT
genomic: TGTCTGCTTGTGGTGGGAAGGTTTCTTTGTTTAACATGATGACATTCAAGgtaatgtcta ... cttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTT
EST: gi|23357522|gb|BU645171.1|BU645171
EST:     TGTCTGCTTGTGGTGGGAAGGTTTCTTTGTTTAACATGATGACATTCAAG                         GTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTT
genomic: TGTCTGCTTGTGGTGGGAAGGTTTCTTTGTTTAACATGATGACATTCAAGgtaatgtcta ... cttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTT
EST: gi|33096311|gb|CF056305.1|CF056305
EST:     TGTCTGCTTGTGGTGGGAAGGTTTCTTTGTTTAACATGATGACATTCAAG                         GTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTT
genomic: TGTCTGCTTGTGGTGGGAAGGTTTCTTTGTTTAACATGATGACATTCAAGgtaatgtcta ... cttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTT

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), 49 (downstream exon)
Score: 110

AGAGGAGGCAGTTCCATGCATTGCACTCTCAAAGAATGATTCCTATGTGATGTCTGCTTGTGGTGGGAAGGTTTCTTTGTTTAACATGATGACATTCAAGgtaatgtcta ... cttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

AGAGGAGGCAGTTCCATGCATTGCACTCTCAAAGAATGATTCCTATGTGATGTCTGCTTGTGGTGGGAAGGTTTCTTTGTTTAACATGATGACATTCAAGgtaatgtcta ... cttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 135

AGAGGAGGCAGTTCCATGCATTGCACTCTCAAAGAATGATTCCTATGTGATGTCTGCTTGTGGTGGGAAGGTTTCTTTGTTTAACATGATGACATTCAAGgtaatgtcta ... cttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

AGAGGAGGCAGTTCCATGCATTGCACTCTCAAAGAATGATTCCTATGTGATGTCTGCTTGTGGTGGGAAGGTTTCTTTGTTTAACATGATGACATTCAAGgtaatgtcta ... cttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatataatcttgagaggaaacaaacatggccttaatcatgcatccttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
                              ccttaat  putative branch site (score: 64)
                                         catccttctt  putative PPT
                                ttaatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctataagcaggtcattagatgcttatataatccataagctggattatataatcttgagaggaaacaaacatggccttaatcatgcatccttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - atgctta
- - - - - - - - - - - - - - - - - - - agctgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgca