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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCTgttcgtgttccccttaccctgctgctttctattgcatttgtttttttctcttattgatttacgtatgtgtgttttgcgtag

Basic information

species Zea mays
transcript GRMZM2G123305_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123305_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g20689.1 (Oryza sativa), 5'ss of exon 2
GCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCTgttcgtgttccccttaccctgctgctttctattgcatttgtttttttc-tcttattgatttacgtatgtgtgttttgcgtag---------------------
||||||||||||||| ||||||||||||||||||||||||| |  |||  ||| |||||||||||  |  ||  || || || ||    |      |  || ||| |||| |||   | | |   | |||||  |  || | | ||| |  |                     
GCCATGCTCGCGTCGATCAAGCTCGAGGTGATGTCGCCCTCCGGTGAGGCCCCCGACGAAGGATCTATTGgtatgt-ttgccgttgatttatcttctcatagtgcttttgctttgcgcgtttggctaatttatctgcgtttctattgtggcgtggtgccgtggtgttctgcag
















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|78109449|gb|DV527865.1|DV527865
EST:     GCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCT                         CTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCC
genomic: GCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCTgttcgtgttc ... ttttgcgtagCTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCC
EST: gi|31359716|gb|CD444073.1|CD444073
EST:     GCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCT                         CTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCC
genomic: GCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCTgttcgtgttc ... ttttgcgtagCTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCC
EST: gi|60400680|gb|DN233487.1|DN233487
EST:     GCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCT                         CTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCC
genomic: GCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCTgttcgtgttc ... ttttgcgtagCTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCC
EST: gi|67041329|gb|CO467584.1|CO467584
EST:     TCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCT                         CTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCC
genomic: GCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCTgttcgtgttc ... ttttgcgtagCTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCC
EST: gi|40334570|gb|CK368640.1|CK368640
EST:     GCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCT                         CTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCC
genomic: GCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCTgttcgtgttc ... ttttgcgtagCTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCC
EST: gi|76293265|gb|DV032833.1|DV032833
EST:     GCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCT                         CTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCC
genomic: GCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCTgttcgtgttc ... ttttgcgtagCTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCC
EST: gi|211040937|gb|FK998650.1|FK998650
EST:     GCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCT                         CTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCC
genomic: GCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCTgttcgtgttc ... ttttgcgtagCTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCC
EST: gi|211189642|gb|FL055471.1|FL055471
EST:     GCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCT                         CTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCCGCTGGTTAGGCCAGGC
genomic: GCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCTgttcgtgttc ... ttttgcgtagCTGTTGAGTTCCACATGCCGCCCATCTGCTCCCC-GCTGGTTAGGCCAGGC

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), 45 (downstream exon)
Score: 49

GCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCTgttcgtgttc ... ttttgcgtagCTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCCGATCTGCGGAGGTGGCACCAGTCATCTCCAAGGCCCTTGAAGACGTTTT


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

GCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCTgttcgtgttc ... ttttgcgtagCTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCCGATCTGCGGAGGTGGCACCAGTCATCTCCAAGGCCCTTGAAGACGTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

GCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCTgttcgtgttc ... ttttgcgtagCTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCCGATCTGCGGAGGTGGCACCAGTCATCTCCAAGGCCCTTGAAGACGTTTT


Block sizes: 33 (upstream exon), 45 (downstream exon)
Score: 9

GCCATGCTCGCGTCGGTCAAGCTCGAGGTGATGTCGCCCTCGGCCGAGTACCCAGACGAAGGATCCGTCTgttcgtgttc ... ttttgcgtagCTGTTGAGTTCCACATGCCGCCCATCTGCTCCCCGCTGGTTAGGCCAGGCCGATCTGCGGAGGTGGCACCAGTCATCTCCAAGGCCCTTGAAGACGTTTT