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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtacccttcaatccttcatctcttccgttcattagttcgccgtcctcgcatcacatcacaaccgcccccctcgtcatcctcaccagGCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCACCAATATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTA

Basic information

species Zea mays
transcript GRMZM2G000623_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000623_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g48030.1 (Oryza sativa), 3'ss of exon 1
gtaggtacccttcaatccttcatctcttccgttcatt---agttcgccgtcctcgcatcacatcacaaccgcccccctcgtc---atcctcaccagGCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCACCAATATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTA
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gttcgtctccttcc-ccatctatcgatccgattcgctttgctttctcaaaccctagattgccttg-aattatccaccaaatccaaatccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA
















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|211283942|gb|FL372041.1|FL372041
EST:     GAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAG                         GCGGTTTCTCC
genomic: GAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAGgtaggtaccc ... tcctcaccagGCGGTTTCTCC
EST: gi|116826509|gb|EC870303.1|EC870303
EST:     GAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAG                         GCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAGgtaggtaccc ... tcctcaccagGCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCA
EST: gi|18176862|gb|BM351795.1|BM351795
EST:     GAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAG                         GCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAGgtaggtaccc ... tcctcaccagGCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCA
EST: gi|18178617|gb|BM379827.1|BM379827
EST:     TACGCAACATGCTCACATCGCCAG                         GCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCA
genomic: TACGCAACATGCTCACATCGCCAGgtaggtaccc ... tcctcaccagGCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCA
EST: gi|211407289|gb|FL458687.1|FL458687
EST:     GAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAG                         GCGGCTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAGgtaggtaccc ... tcctcaccagGCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCA
EST: gi|60352141|gb|DN219114.1|DN219114
EST:     GAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAG                         GCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAGgtaggtaccc ... tcctcaccagGCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCA
EST: gi|16926289|gb|BM079357.1|BM079357
EST:     GAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAG                         GCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCA
genomic: GAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAGgtaggtaccc ... tcctcaccagGCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCA

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: 96

GGCGTCGTCAAGCTCATCAGCGCCGAGGGCTTCGAATTCGTCGTCGACAAGAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAGgtaggtaccc ... tcctcaccagGCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCACCAATATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 136

GGCGTCGTCAAGCTCATCAGCGCCGAGGGCTTCGAATTCGTCGTCGACAAGAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAGgtaggtaccc ... tcctcaccagGCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCACCAATATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

GGCGTCGTCAAGCTCATCAGCGCCGAGGGCTTCGAATTCGTCGTCGACAAGAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAGgtaggtaccc ... tcctcaccagGCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCACCAATATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

GGCGTCGTCAAGCTCATCAGCGCCGAGGGCTTCGAATTCGTCGTCGACAAGAAGGCCGCCATGGTCTCCAACACCCTACGCAACATGCTCACATCGCCAGgtaggtaccc ... tcctcaccagGCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCACCAATATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagttcgccgtcctcgcatcacatcacaaccgcccccctcgtcatcctcaccagGCGGTTTCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCACCAATATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTA
                                 cccccctcgtcatcct  CT-rich tract