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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggctcagatcacatctccaacgaactcactcgttcgttcgcattgggttacttgctgatgattggcgctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAGGTGAACCCCAAGGAGGTCATCGTCGGATG

Basic information

species Zea mays
transcript GRMZM2G025214_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025214_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g01450.1 (Oryza sativa), 3'ss of exon 1
--------------------------gtcggctcag-atcacatctccaacgaactcactcgttcgttcgcattgggttacttgctgatgattggcgctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAGGTGAACCCCAAGGAGGTCATCGTCGGATG
                           || || | | ||||      | | |   | |||  ||| | |    | | || | ||    ||  |  |     |  |||| ||  |||||||||| |||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || |||||
gtaaactataaatatctctcttctccttccgcccggcatcatcagatctagggttttacttcttcttcca---ttgattccctgaacttgcctttctaatgttaagGTTGCTCTCGACATCGAGTACCACCACAACATGTATGCGTCGCACCACAAGGTCAACCCCAAGGAAGTCATTGTTGGATG
















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|211273471|gb|FL057446.1|FL057446
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|211273466|gb|FL057441.1|FL057441
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|211273460|gb|FL057435.1|FL057435
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|149083162|gb|EE172426.2|EE172426
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|211273468|gb|FL057443.1|FL057443
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|26558673|gb|CA830908.1|CA830908
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|211273470|gb|FL057445.1|FL057445
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|211273463|gb|FL057438.1|FL057438
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|15590011|gb|BI674627.1|BI674627
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|91875888|gb|EB405845.1|EB405845
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATC
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATC
EST: gi|71333209|gb|DR803652.1|DR803652
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCACCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|211217401|gb|FL057434.1|FL057434
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|211273461|gb|FL057436.1|FL057436
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|110943385|gb|EE163542.1|EE163542
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|211273469|gb|FL057444.1|FL057444
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|89250749|gb|DY622535.1|DY622535
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|71768478|gb|DR966415.1|DR966415
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|211273465|gb|FL057440.1|FL057440
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|211273467|gb|FL057442.1|FL057442
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|89754710|gb|DY685406.1|DY685406
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAAAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|211117498|gb|FL139017.1|FL139017
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|211273462|gb|FL057437.1|FL057437
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|74233131|gb|DT641045.1|DT641045
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|23199556|gb|BU582121.1|BU582121
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|22546037|gb|BU098358.1|BU098358
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|211273464|gb|FL057439.1|FL057439
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
EST: gi|91879003|gb|EB408960.1|EB408960
EST:     TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAG                         GTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG
genomic: TCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAG

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: 173

GGACCGCGTCATCGGCACCCTCCTCGGTTCCCTCCTCTCCGACGGCACCGTCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAGGTGAACCCCAAGGAGGTCATCGTCGGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 161

GGACCGCGTCATCGGCACCCTCCTCGGTTCCCTCCTCTCCGACGGCACCGTCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAGGTGAACCCCAAGGAGGTCATCGTCGGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

GGACCGCGTCATCGGCACCCTCCTCGGTTCCCTCCTCTCCGACGGCACCGTCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAGGTGAACCCCAAGGAGGTCATCGTCGGATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 98

GGACCGCGTCATCGGCACCCTCCTCGGTTCCCTCCTCTCCGACGGCACCGTCCACGTCCGCAACTCCTATGTCGTCCCCCACAGCGAGTCAGCCGACCAGgtcggctcag ... gctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAGGTGAACCCCAAGGAGGTCATCGTCGGATG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggctcagatcacatctccaacgaactcactcgttcgttcgcattgggttacttgctgatgattggcgctgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAGGTGAACCCCAAGGAGGTCATCGTCGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG