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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctccacgcactctgagttcaaacagtgttgtcagatccctgtctgatcttttacctttttattattctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT

Basic information

species Zea mays
transcript GRMZM2G068392_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068392_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g68010.3 (Oryza sativa), 3'ss of exon 5
gtaaatctccacgcactctgagttcaaacagtgttgt---cagatccctgtctgatcttttacctttttattattctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT
|| || ||||||    ||| |||  |||||| ||| |   ||||  |||| |||||| |    |        || || ||||||||||| |||||||| ||||| | |||||||| ||||||||||| |||||| | ||||||||||||||||||||| |||||||||| ||||||||||| |
gtgaa-ctccacta--tctaagtctaaacagagttctgctcagaaacctgactgatcataggtc--------atccttaccagGAATCTCTGAAAAATATACTGATTATCTTTGCAAAGCTGAATGCCGGAATACGTTATGTACAAGGGATGAATGAAATTTTGGCACCTCTCTTCTTTGTGT

upper sequence: GRMZM2G068392_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G00430.2 (Glycine max), 3'ss of exon 5
-gtaaatctccacgcactctgagttc--aaacagtgttg--tcagatccctgtctgatc-ttttacctttttattattc-----tcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT
  |    ||| |   | | | | ||   ||    ||     || |  |  | |||   | ||||  ||||  | | |||     |   |||||  |||| || |   || |  |  | ||||| ||| ||||  | || ||||||||| | ||||||||||||||||| ||||| || ||||||| ||| |
gttcttcctctatttatttttattttcgaattcatgccaactcggtcctttttcttgccattttgactttcaacttttccggattttgcagGAGGCTTTAAAGACCATATTAATTGTTTTTGCAAAGTTGAACTCGGGTATAAGATATTTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT

upper sequence: GRMZM2G068392_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G36520.1 (Glycine max), 3'ss of exon 5
----------------gtaaatctccacgcactctgagttcaaa-cagtgttgtcagatccctgtctgatcttttacctttttattattctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT
                 ||| | |     ||   | |   |||  || |  | |    | ||  | ||| |||| | |||||    ||| |   |||||  |||| || |   || |  | || ||||| ||| ||||  | || ||||||||||| ||||||||||||||||| ||||| || ||||||| ||| |
gttcttcctctattttttaattttattttcaaattcataccaactcaatcctttttcttgccattttga-ctttcaacttttccggattttt--cagGAGGCTTTAAAGACCATATTAATTATTTTTGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGT

upper sequence: GRMZM2G068392_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 5
-----------------gtaaatctccacgcactctgagt--tcaaa----cagtgttgtcagatccctgtctgatcttttacctttttattattctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT
                  || |  |  | ||  |  |  |  | |||    |||| |  | | |    |   ||   |||||    | | ||       | ||||  ||||||| ||  |  ||   || || || ||| ||||| |||| || |||||||||||||||||||||||  | ||||||||  | ||||   | |
gttgggtgttggttttgctatagtttaaagcctttgggatgattaaaacatcagtatactgatagtttttcttgtctttttatacatgttttgcatgt-ctagGATGCTTTGAAGAACATTTTGACTATTTTCGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCT

upper sequence: GRMZM2G068392_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 5
gtaaatctccacgcactctgagttcaaacagtgttgtcag-atc-cctgtctgatctt-ttacctttttattattctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT
    || |      |||    |    |    || |   |  ||| ||  | ||| |   |||  |   |  | |  |   |||||  ||||||  ||  || || |  | ||||| ||| ||||| | || ||||||||||| ||||||||||||||| ||||||| || || |||| |||||
--gtatgtgttgttacttgaggcatgagacttgatacaaacatcacccatttgaccaaattaaatggatcctgtattt--cagGATGCTTTGAGGAACATATTGATTGTGTTTGCAAAGTTGAATCCGGGTATAAGATATGTGCAAGGGATGAATGAAATTTTGGCGCCTCTATTCTATGTAT

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|148935027|gb|EC879068.2|EC879068
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
EST: gi|71433967|gb|DR815017.1|DR815017
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
EST: gi|113817914|gb|DW939072.1|DW939072
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGC
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGC
EST: gi|50324142|gb|CO519268.1|CO519268
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
EST: gi|50331565|gb|CO526691.1|CO526691
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
EST: gi|38502614|gb|CF972474.1|CF972474
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
EST: gi|50331308|gb|CO526434.1|CO526434
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATA
EST: gi|44681890|gb|CK786938.1|CK786938
EST:     CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAG                         GAATCTTTGAAAAATGTACTGTTAATCTTCGTTGCCAAGCTGAAATGCTGG
genomic: CTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTT--T-GCCAAGCTGAA-TGCTGG

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: 175

TACTCAGAGATTATGGAGCAGATTGACCGCGATGTAAAGCGCACCCACCCTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

TACTCAGAGATTATGGAGCAGATTGACCGCGATGTAAAGCGCACCCACCCTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 100

TACTCAGAGATTATGGAGCAGATTGACCGCGATGTAAAGCGCACCCACCCTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 87

TACTCAGAGATTATGGAGCAGATTGACCGCGATGTAAAGCGCACCCACCCTGACATGCAGTTCTTCTGCGGCGACTCGTCTTTTGCAAAGTCCAATCAGgtaaatctcc ... ttctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacagtgttgtcagatccctgtctgatcttttacctttttattattctcaccagGAATCTTTGAAAAATGTACTGTTAATCTTTGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTAT
                     gtctgat  putative branch site (score: 87)
                           tcttttacctttttat  CT-rich tract
                          atcttttaccttttta  TA-rich tract