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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGAAGAGATCCACCCTACAGCTATTCTCAGTGTAGTTGCCAATCTGACACCTTGGTCTGATCACAACCAAAGTCCTAGGAACATGTACCAATGCCAGgttagtactcagaagtcagatcttgtccttatagtgattggttgatcatgctttcctttttggactaacccccagtcatcctccttgtttgcag

Basic information

species Zea mays
transcript GRMZM2G388892_T01
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G388892_T02 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os10g35290.1 (Oryza sativa), 5'ss of exon 17
TCATGAAGAGATCCACCCTACAGCTATTCTCAGTGTAGTTGCCAATCTGACACCTTGGTCTGATCACAACCAAAGTCCTAGGAACATGTACCAATGCCAGgttagtactcagaagtc----------agatcttgtccttatagtgattgg---ttgatcatgcttt-------------cctttttggactaaccc--ccagtcatcctccttgtttgcag
||||||||| |||||||||||||| ||||| ||||||||||| ||| |||||||||||||||||||||| ||||||||| |||||||||||||||| ||||| ||||  ||||  |           | |||   | || ||    | ||    ||| ||| || |              |||||||   |||  ||  | |  |  | | ||||||  |||
TCATGAAGAAATCCACCCTACAGCCATTCTTAGTGTAGTTGCAAATTTGACACCTTGGTCTGATCACAATCAAAGTCCTCGGAACATGTACCAATGTCAGgtcagtagccagatcttcccttactgtaaatcaatttctcatgcataatgaaaattgctcacgcataatgaatgctgagaccttttttttctagacctgctaacctgcttgcttgttcacag

upper sequence: GRMZM2G388892_T02 (Zea mays), 5'ss of exon 18
lower sequence: AT1G29940.1 (Arabidopsis thaliana), 5'ss of exon 19
TCATGAAGAGATCCACCCTACAGCTATTCTCAGTGTAGTTGCCAATCTGACACCTTGGTCTGATCACAACCAAAGTCCTAGGAACATGTACCAATGCCAGgttagtactcagaagtcagatcttgtccttatagtgattggttgatcatgctttcctttttggactaacccccagtcatcctccttgtttgcag
||| || || || || || || |  ||  | ||||| ||||| ||||| ||||||||||| ||||| |||||||||||  | |||||||| || || ||||| | |||| |||| |  |||       || || |||||     ||  ||||     ||||  |  ||    |||| || |             
TCACGAGGAAATTCATCCAACCGGGATGATAAGTGTGGTTGCTAATCTTACACCTTGGTCAGATCATAACCAAAGTCCCCGTAACATGTATCAGTGTCAGgt-attact-agaaattcgatgcaaatttttta-tgatt-----atgctgctggaagtttttta--aattttcagttatacag-----------

upper sequence: GRMZM2G388892_T02 (Zea mays), 5'ss of exon 18
lower sequence: Vv13s0084g00600.t01 (Vitis vinifera), 5'ss of exon 18
TCATGAAGAGATCCACCCTACAGCTATTCTCAGTGTAGTTGCCAATCTGACACCTTGGTCTGATCACAACCAAAGTCCTAGGAACATGTACCAATGCCAGgttagtactcagaagtca---gatcttgtccttatagtgattggttgatcatgctttccttt--ttggactaacccccag---tcatcctccttgtttgcag----------------
||||||||||||||| || || |  || |||||||| ||||| | ||| ||||||||||| ||||||||||| || ||  | || |||||||| || ||||||  | ||   | ||     ||    |  | |||| ||  |  | | || || | || |    ||  ||||||         |  |  || |  ||| |                  
TCATGAAGAGATCCATCCCACTGGAATGCTCAGTGTTGTTGCTAGTCTTACACCTTGGTCGGATCACAACCAGAGCCCGCGTAATATGTACCAGTGTCAGgttttttcttgcatgttgactgaaaaaggtcctataatgtattat-gctcctgttatcttcaaatttaactaactgttgtgttttgttttcttctttttctcttaaaatgattggtag

upper sequence: GRMZM2G388892_T02 (Zea mays), 5'ss of exon 18
lower sequence: EFJ24096 (Selaginella moellendorffii), 5'ss of exon 5
TCATGAAGAGATCCACCCTACAGCTATTCTCAGTGTAGTTGCCAATCTGACACCTTGGTCTGATCACAACCAAAGTCCTAGGAACATGTACCAATGCCAGgttagtactcagaagtcagatcttgtccttatagtgattggttgatcatgctttcctttttggactaacccccagtcatcctccttgtttgcag
|||    ||  | || || || |||||  | ||||| ||||| |   | ||||||||||| |||||||| ||||||||| | || |||||||| |||||||||  |||          || |  |      || || || |||  ||   |  |   |   |                                
TCACATTGAACTGCATCCGACGGCTATGTTGAGTGTGGTTGCAAGCTTAACACCTTGGTCGGATCACAATCAAAGTCCTCGAAATATGTACCAGTGCCAGgtttatac----------gagc--gctaccgtaatgtttagtttttctaacagtttctacag--------------------------------

upper sequence: GRMZM2G388892_T02 (Zea mays), 5'ss of exon 18
lower sequence: EFJ04457 (Selaginella moellendorffii), 5'ss of exon 18
TCATGAAGAGATCCACCCTACAGCTATTCTCAGTGTAGTTGCCAATCTGACACCTTGGTCTGATCACAACCAAAGTCCTAGGAACATGTACCAATGCCAGgttagtactcag---aagtcagatcttgtccttatagtgattggttgatcatgctttcctttttggactaacccccagtcatcctccttgtttgcag
|||    ||  | || || || |||||  | ||||| ||||| |     ||||||||||| |||||||| ||||||||| | || |||||||| |||||||||  |||       |  |||  | | ||  || ||    ||  |  |                                                 
TCACATTGAACTGCATCCGACGGCTATGTTGAGTGTGGTTGCAAGCTCAACACCTTGGTCGGATCACAATCAAAGTCCTCGAAATATGTACCAGTGCCAGgtttatacgagcgctacatcacgtttagtttttctaacagtttctacag------------------------------------------------

upper sequence: GRMZM2G388892_T02 (Zea mays), 5'ss of exon 18
lower sequence: EFJ35146 (Selaginella moellendorffii), 5'ss of exon 19
TCATGAAGAGATCCACCCTACAGCTATTCTCAGTGTAGTTGCCAATCTGACACCTTGGTCTGATCACAACCAAAGTCCTAGGAACATGTACCAATGCCAGgttagtactcagaagtcagatcttgtccttatagtgattggttgatcatgctttcctttttggactaacccccagtcatcctccttgtttgcag
|||    ||  | || || || |||||  | ||||| ||||| |     ||||||||||| |||||||| ||||||||| | || |||||||| |||||||||  |||          || |  |      || || || |||  ||   |  |   |   |                                
TCACATTGAACTGCATCCGACGGCTATGTTGAGTGTGGTTGCAAGCTCAACACCTTGGTCGGATCACAATCAAAGTCCTCGAAATATGTACCAGTGCCAGgtttatac----------gagc--gctaccgtaatgtttagtttttctaacagtttctacag--------------------------------

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), 47 (downstream exon)
Score: 150

TCATGAAGAGATCCACCCTACAGCTATTCTCAGTGTAGTTGCCAATCTGACACCTTGGTCTGATCACAACCAAAGTCCTAGGAACATGTACCAATGCCAGgttagtactc ... ttgtttgcagATGGCAAAGCAGACCATGGGTTTTTGCGGACAGGCCCTAAAATTCCGTACTGATGTAAAAGCATTCCATCTACAG


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 58

TCATGAAGAGATCCACCCTACAGCTATTCTCAGTGTAGTTGCCAATCTGACACCTTGGTCTGATCACAACCAAAGTCCTAGGAACATGTACCAATGCCAGgttagtactc ... ttgtttgcagATGGCAAAGCAGACCATGGGTTTTTGCGGACAGGCCCTAAAATTCCGTACTGATGTAAAAGCATTCCATCTACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 62

TCATGAAGAGATCCACCCTACAGCTATTCTCAGTGTAGTTGCCAATCTGACACCTTGGTCTGATCACAACCAAAGTCCTAGGAACATGTACCAATGCCAGgttagtactc ... ttgtttgcagATGGCAAAGCAGACCATGGGTTTTTGCGGACAGGCCCTAAAATTCCGTACTGATGTAAAAGCATTCCATCTACAG


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 58

TCATGAAGAGATCCACCCTACAGCTATTCTCAGTGTAGTTGCCAATCTGACACCTTGGTCTGATCACAACCAAAGTCCTAGGAACATGTACCAATGCCAGgttagtactc ... ttgtttgcagATGGCAAAGCAGACCATGGGTTTTTGCGGACAGGCCCTAAAATTCCGTACTGATGTAAAAGCATTCCATCTACAG