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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttccatgcacttttagtcaattattcaattgcattcctcaaagtagttcctaacattgatgtttggaatgtccttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC

Basic information

species Zea mays
transcript GRMZM2G379577_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G379577_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 7
gtattttccatgcactt--ttagtcaattattcaattgcattcctcaaagtagttcctaacattgatgtttggaatgtccttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC
||| ||||  |   | |  ||| |||| |    || ||   |     |      | || |||   |||| ||| ||  ||||||||| | || ||||| ||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||| |||||||||||||||| ||||| |||||||
gtagtttctgtcttcctctttaatcaaatgca-aactgtgataagtgataagtgttctgacaactatgtatggcataaccttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC

upper sequence: GRMZM2G379577_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os09g36180.1 (Oryza sativa), 3'ss of exon 8
gtattttc-catgcacttttagtcaattattcaattgcattcctcaaagtagttcctaacattgatgtttggaatgtccttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC
||| ||||   | |  ||||| |||| |    | |   ||       | | |||| |||||   || | ||| ||   |||||||| | || ||||| ||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||| |||||||||| ||||| ||||| |||||||
gtagtttcgtcttcctttttaatcaagtgcaaagtgtgat-------aattgttc-taacagctatctatggcataatcttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCTCCTGGGAAGGCCACCATCC

upper sequence: GRMZM2G379577_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA09G40260.1 (Glycine max), 3'ss of exon 8
----------------------------------------------------------------------------------------------------------gtattttccatgcacttttagtcaattattca----attgcattcctcaaagtagttcctaacat-tgatgtttggaatgtc--cttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC
                                                                                                           ||||||   ||  |  |   ||  | | |||    ||   ||   | ||  | |     |  || | |||||||     ||  | || ||| | ||   ||| ||||| || || ||||| ||||| ||  |||| |||||||||||||||||||||||| || |||| || ||||| || ||||| ||| 
gtgacttaaacagtcttttaccataccagtgtgtatgtgcatgtctatatagatattcttttatatagatgatgaataatttgtgcttgcactgtacaacccggacatattttgtttgtgcagtgcatccctgactcagtaaataatataattaaactttgccttcattatcttatgtttgtgtcttcaacattgcagGATCCTTCGAAGCATGTGTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTTTGTTGAATCCTCCTGGAAAAGCTACAATCA

upper sequence: GRMZM2G379577_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA07G08910.1 (Glycine max), 3'ss of exon 5
---------gtattttccatgcac-----ttttagtcaattattcaattgcattcctcaaagtag--ttcctaacattgatgtttggaatgtccttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC
          |||  | ||||        | |   | | ||| | ||||  | |  | |||  ||   || |||| ||| | || |   |   | || ||| | ||    || |||||||| || ||||| || || ||  |||| ||||||||||||||||||||||||||  | ||||| ||||  || ||||| ||||
gcaccaaaaatatcgtgcatgtgaaagtgtatctatgatttagtaaattatacttttaaaaccaggcctcataactttgttatt-gtcttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC

upper sequence: GRMZM2G379577_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA18G45750.1 (Glycine max), 3'ss of exon 7
----------------------------------------------------------------------------------------------------------------gtattttcc-atgcacttttagtcaattattcaattgcattcctcaaagtagttcctaacat-tgatgtttggaatgtcct---tttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC
                                                                                                                 | ||| |   ||||    |    || ||   |||   ||   | ||  | |     |  || | ||||| |     |||    ||  || | ||   ||| ||||| || || ||||| ||||| ||  |||| |||||||||||||||||||||||| || |||| || ||||| || ||||| ||| 
gtgacttggactgtctttttccataccagtgtgtgtgtacatgtctgtatagtgaatttttttttatagatgatgaataatttgtgcttgcactgtacaacccggacatagtttgtttgcttgtgcatccctgacaaaata---aataatataattaaactttgccttcattatcttatgttcgtgtcttccaacgttgtagGATCCTTCGAAGCATGTGTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTTTGTTGAATCCTCCTGGAAAAGCTACAATCA

upper sequence: GRMZM2G379577_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA03G02250.1 (Glycine max), 3'ss of exon 13
--------------------------------------------------------------------------------------------------gtattttccatgcac-----ttttagtcaattattcaattgcattcctcaaagtagttcctaaca-ttgatgtttggaatgtccttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC
                                                                                                   |||  | ||||        | |   | | ||| | ||||  |||  | |||  ||  |  |  | ||  | | ||   |     || ||| | |||  |||  ||||||| || ||||| ||||| ||  |||| ||||||||||||| ||||||||||||  | ||||| ||||| || ||||| ||||
gtgacttgggctgtctttttaaccataccagtatttgtgtgcaagttcattgtttccttttatagattgcaaataagggtgccttgaccatggtcaacatatcgtgcatgtgaaagtgtatctatgatttagtaaattatattattaaaaccaggcctcataacttagtttctgtcttcaatgttgcagGATCCATCGAAGAATGTTTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAGCATGTGGTTTCTTTTAAACCCTCCTGGAAAAGCTACAATCC

upper sequence: GRMZM2G379577_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT2G46480.1 (Arabidopsis thaliana), 3'ss of exon 3
gtattttccatgcacttttagtcaattattcaattgcattcctcaaagtagttcctaacattgatgtttggaatgtccttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC
||| |   ||  | ||  || |   ||     | |   | | | |||       || |||  |   |   |  | |  ||  ||| | ||    |  ||||||||||| ||||||||||| ||| | ||||||||||| ||||  |||||||||||| ||||||| |||||  | || |||||||
gtaatgatcaatccctagtaattg-ttgcaagaataagtgctttaaa-------cttacaa-ggcctactgggtttatttggcagGATCCTTCAAGGCATGTTTTCCACCTTGTGACTGATAAGCTCAACTTTGGAGCAATGAGTATGTGGTTTCTGTTGAACCCTCCTGGAGAAGCGACCATCC

upper sequence: GRMZM2G379577_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv15s0048g01300.t01 (Vitis vinifera), 3'ss of exon 8
-----gtattttccatgcacttt--tagtcaattattcaattgcattcctcaaagtagttcctaa-cattgat---gtttgg-aatgtcct---tttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC
      ||      | |   |||  |||  ||  |   ||  ||||  |  |   |  | | |   |||| |    |||||  |||  |||   || ||| ||||||| |||||||| |||||||| || ||||| ||| | || |||||||||||||| |||||||||||| ||||||| || || || || || ||||
tttggataagcgaaaggggatttgttaggaaagcacaaaagggcatcacatatgttcttcctttttcattcactaagtttgctaataccctcgattgcagGAACCAGAAAAACATGTATTCCATCTGGTTACTGATAAGCTGAATTTTGGAGCCATGAATATGTGGTTTCTGTTGAACCCCCCAGGAAAAGCAACTATCC

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: 45 (upstream exon), 42 (downstream exon)
Score: 14

TGAAAATTTAGAAAATCCAAATCTCTATCACTATGCACTTTTCTCAGATAATGTCTTGGCAGCTTCTGTTGTTGTGAACTCAACCATCATGAATGCTAAGgtattttcca ... tccttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC


Block sizes: 26 (upstream exon), 42 (downstream exon)
Score: 4

TGAAAATTTAGAAAATCCAAATCTCTATCACTATGCACTTTTCTCAGATAATGTCTTGGCAGCTTCTGTTGTTGTGAACTCAACCATCATGAATGCTAAGgtattttcca ... tccttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC


Block sizes: 45 (upstream exon), 30 (downstream exon)
Score: 6

TGAAAATTTAGAAAATCCAAATCTCTATCACTATGCACTTTTCTCAGATAATGTCTTGGCAGCTTCTGTTGTTGTGAACTCAACCATCATGAATGCTAAGgtattttcca ... tccttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC


Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 5

TGAAAATTTAGAAAATCCAAATCTCTATCACTATGCACTTTTCTCAGATAATGTCTTGGCAGCTTCTGTTGTTGTGAACTCAACCATCATGAATGCTAAGgtattttcca ... tccttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattgcattcctcaaagtagttcctaacattgatgtttggaatgtccttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC
                                           tgtccttttc  CT-rich tract
                         taacatt  TA-rich tract