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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgctgaatctgaacctactatctttacatttttatagatgattcaacatcaccaacttatgttccaaattttatggtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA

Basic information

species Zea mays
transcript GRMZM2G404207_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
gtacgctg-aatctgaacctactatctttacatttttatagatgattcaacatcaccaacttatgttccaaattttatggtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
||| | |   |||||||  || ||||||   |  |   ||| || || ||||||  || ||||      |||  |||||   || | || ||||||| ||||| |||||||| ||||||||||| |||||||| |||||||||||||| |||||||| || || || ||||||||||| ||||| || | ||||
gtaagttttgatctgaaattattatcttactacct--gtagttggtt-aacatcctcaccttaa-----aaagattatg---aactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA

upper sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G16380.1 (Glycine max), 3'ss of exon 9
---------gtac-gctgaatctgaacctactatctttacatttttatagatgattcaacatcaccaactta-tgttccaaattttatggtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
          |||  ||   ||  |||||| | | |  |  |  ||   |||  ||||  ||||   | ||  ||    | || |  |    || ||    ||| || || || || || |||||||||||||| |||||||| || |||||||||||||||||||| || || ||||| ||||||||  | || || |  |||
attgcaatattaccacttggtcgaaacctattttttccagctggtt---gatt-ttcactatcatgcatttgctgacatatatatcttttgaaaattgatgtagTTATGTGGCGCCGGAGTATGCAATGACTGGGCATCTTCTTGTTAAGAGTGATGTTTACAGCTATGGTGTTGTTCTTCTTGAGCTTTTGACTGGAAGAAAA

upper sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G02800.1 (Glycine max), 3'ss of exon 8
----------------------------------------------------------------------------------gtacgctgaatctgaacctactatcttta-catttttatagatgattcaacatcaccaact---tatgttcca-------------aattttatg-----gtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
                                                                                     |  |  ||   | | |  | | |||| ||   || ||   |  |  |||| ||||  |   |   || |               ||||| ||     |    | |||   || ||||| || ||||||||||||||||| ||||||||||| || || ||||||||||||||||| || || || |||||||||||||| || || |  || 
gtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagcttcttgtgtttatcagacttttatgcggatatacattaccatttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG

upper sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G07140.1 (Glycine max), 3'ss of exon 9
-------gtacgctgaatctgaacc-tactatctttacatttttatag-atgattcaacatcaccaacttatgttccaaattttatggtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
        |    ||  ||  |||  |  ||  | |   || || ||  || ||| |    |    |  ||| |||     | | ||   || | |||  || || || || || || ||||||||||| || |||||||| || |||||||||||||||||||| || || || |||||||||||  | || || |  |||
ctgaactattttttgtttcaaaactattgtaattctttgttgttttactattatttactccctgatatatatattctttcatatttgaaaaactattc--agTTATGTGGCTCCGGAGTATGCAATGACGGGACATCTTCTTGTGAAGAGTGATGTTTACAGCTATGGTGTTGTCCTCCTTGAGCTTTTGACCGGAAGAAAA

upper sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G20590.1 (Glycine max), 3'ss of exon 9
gtacgctgaatctgaacctactatctttacatttttatag-atgattcaaca--tcaccaacttatgttccaaatt----ttatggtcaatttttctt--agGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
 || | ||  |  |    |   || |  |   ||||||   ||   | ||||  ||  |||  |     | |||||    | || | ||  || | ||  || ||| | || |||||||||||||||||||||||||||||||| |||||||||||||| || || || || || |||||||||||||| || || |  || 
ttaagttg--ttaggtgatgtcatttaaaaggttttatttcatctcttaacagttcctcaagatgaaaactaaattcatctcattgacatgttgttttgcagCTACTTAGCTCCTGAATATGCAATGACTGGCCATCTTCTGGTCAAGAGTGATGTTTATAGTTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG

upper sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G18470.1 (Glycine max), 3'ss of exon 8
------gtacgctgaatctgaacctactatctttacatttttatagatgatt-caacatcaccaacttatgttccaaattttatggtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
        |   |   |   || ||| | |  ||   | ||  |  |  |||    | || |  |  ||| ||     |  |||    ||   |  | || || || || || || |||||||||||||| |||||||| || ||||| ||||||||||| || || || || |||||||||||  | || || |  |||
ctgaactaattattgtttcaaaactattgtaattctttgttgttttactattatgccctccctgatatatattttctttcatatttgaaaaactattcagTTATGTGGCCCCAGAGTATGCAATGACTGGACATCTTCTTGTGAAGAGCGATGTTTACAGTTATGGTGTTGTCCTCCTTGAGCTTTTGACTGGAAGAAAA

upper sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G42600.1 (Glycine max), 3'ss of exon 4
---gtacgctgaatctgaacctac-tatctttacatt----tttatagatgattcaacatcaccaacttatgttccaaattttatggtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
      || ||||  |     |||  |  | ||||||    ||| |      |||  |   |  ||  |   ||       |||   ||  | |||   || || || || |||||||||||||||||||| ||||| || || || ||||||||||||||||| || || || |||||||||||||| |  || |  || 
agatcccggtgaacttttttttacacagatatacattaccatttctgtgcatttcctctagatgaaactgattttttgccattaaaatct-tgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAAGTGGAAGAAAG

upper sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G01210.1 (Glycine max), 3'ss of exon 10
----------gtacgctgaatctgaacctactatctttacatttttatagatgattcaacatcaccaacttatgttccaaattttatggtcaatttttctt--agGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
              | ||      ||     |   |||    | |||   ||   | || || |  ||  |   |||   || | || | ||  || | ||  || ||| | || |||||||||||||||||||||||||||||||| |||||||| ||||| || || || || || |||||||||||||| || || |  || 
ttaagtggttaggtgatggcatgtaaaaggtttcatttcagctcttaacaattccttaaaatga--aaactgcattc---atctcattgacatgttgttttgcagCTACTTAGCTCCTGAATATGCAATGACTGGCCATCTTCTGGTCAAGAGTGACGTTTATAGTTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG

upper sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G56890.1 (Arabidopsis thaliana), 3'ss of exon 13
gtacgctgaatctgaacctactatctttacatttttatagatgattcaacatcaccaacttatgttccaaattttatg---gtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
||| | | |     || | |  |||  ||||   |  |  |   |      |  ||   |    ||  || || |||    ||   ||| |  |||||| || ||||| ||||| |||||||| || |||||| |||| ||||||||||| || || ||||| || || || || ||||| |||||||||  ||||
gtaagataa--taaaaaccagaatcggtacaaactgcttcagactgttttttttcctgttccgattttaacttatataaatgttgctttctaatagGTATGTGGCACCGGAATACGCAATGACAGGGCATCTTTTGGTGAAGAGTGATGTGTATAGTTACGGAGTTGTGCTTCTCGAGCTACTTACAGGGCGGAAA

upper sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv11s0016g02150.t01 (Vitis vinifera), 3'ss of exon 11
-------------gtacgctgaatctgaacctactatctttacatttttatagatgattcaacatcaccaacttatgttccaaattttatggtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
              |    |   | | |  |  || | | |   ||||| |      || ||  | |      | |  ||| ||||  ||  |   ||    | ||||| || || || || ||||||||||||||||||||||| || |||||||||||||| ||||| || ||||| || ||||||||||| ||||| |  |||
atattcctgctttctttaatatttttaagtcccctgtttgtgtcttttttt----tttttaattttatgtctctgttctcctaatt--attattttttcccatcagGTATGTGGCTCCAGAGTATGCAATGACTGGCCATCTTCTTGTGAAGAGTGATGTTTATAGCTATGGAGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAA

upper sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0002g02220.t01 (Vitis vinifera), 3'ss of exon 9
-gtacgctgaatctgaacc-tactatcttta---catttttatagatgattcaacatcaccaacttatgttccaaattttatggtcaatttttctt--agGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
  ||   ||  | || ||  || | |||||    | || || ||     ||   | |||  | || | ||  |  ||   ||   |   || | ||  || ||| | || || |||||||||||||||||||||||||| || || |||||||||||||| || || ||||| || ||||||||||| ||||| |  || 
tatattttgcctgtggacggtagtttctttttctcgttgttttattgctttgtgcttcaaaatctcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG

upper sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S343_14V6.1 (Physcomitrella patens), 3'ss of exon 7
gtacgctgaatct--gaacctactatcttt-acatttttatagatgattcaacatcacca--acttatgttccaaattttatggtcaatttttctt--agGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
 |    || ||    |   || |||| ||| | || | | | | ||   |   | |      ||||   | |   | ||  || |  |||| |  |  ||||| || || |||||||| |||||||| || ||||| || || ||||||||||||||||| ||||| ||||| || || ||||||||  | ||   ||||
ttctcttgtattctcgtttcttctattttttagatatctttggctggaccgctagcgttgttacttgattcctgcacttactgattgatttctactgcagGTATGTGGCCCCTGAATACGCAATGACAGGGCATCTACTTGTGAAGAGTGATGTTTACAGTTACGGAGTAGTGCTTCTAGAGCTCCTCTCTGGACGGAAA

upper sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S95_115V6.1 (Physcomitrella patens), 3'ss of exon 7
-----gtacgctgaatctgaacctactatctttacatttttatagatgattcaacatcacc--aacttatgttccaaattttatggtcaatttttctt--agGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
      |||  || | |   | |||  |     |||||  |    |||     || |  ||     || ||  |  |  | | ||||  |||     |  ||||||||||| ||||| || |||||||| || |||||||| || ||||| || |||||||| || || || || || |||||||||||  | ||   ||||
ttcttttacattggacc-acatctagaactaccacattaatcagaatgtcaggacttagccttggtttctgcactgacctat-tggttgattcaaactgcagGTACGTTGCCCCTGAGTACGCAATGACAGGACATCTTCTTGTTAAGAGCGACGTTTACAGTTATGGAGTGGTACTTCTTGAGCTCCTCTCGGGACGGAAA

upper sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
----gtacgctgaatctgaacctactatctttacatttttatagatgattcaacatcaccaacttat--gttccaaattttatggtcaatttttctt--agGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
    ||| | |     |  || |  || ||||||||  | | |         | ||      ||| |  |  | || |   |   | |||   |  |  ||||| || |||||||||||||| ||||| ||||| ||||| |||||||| || || |||||||| || || || || ||||| || ||| | |||| ||  
accagta-gttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG

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: 47 (upstream exon), 49 (downstream exon)
Score: 64

AACATGACTTCACCCCAAAGGTGTCGGACTTCGGCTTAGCAAGGACAGCTCTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTTATGGGAACTTTTGGgtacgctgaa ... tttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 43

AACATGACTTCACCCCAAAGGTGTCGGACTTCGGCTTAGCAAGGACAGCTCTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTTATGGGAACTTTTGGgtacgctgaa ... tttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 59

AACATGACTTCACCCCAAAGGTGTCGGACTTCGGCTTAGCAAGGACAGCTCTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTTATGGGAACTTTTGGgtacgctgaa ... tttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 75

AACATGACTTCACCCCAAAGGTGTCGGACTTCGGCTTAGCAAGGACAGCTCTGGGTGAGGGAAACGAGCATATTTCAACTCGTGTTATGGGAACTTTTGGgtacgctgaa ... tttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgattcaacatcaccaacttatgttccaaattttatggtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
                                             tttttctt  CT-rich tract
                                           aatttttctta  TA-rich tract