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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggttggctcacaactatgccgatgtagtttactattgtaatatctttatcgacggatatcgacaaactgatccacactatacagGTATATGGGTATGGGGTTCCCCCGTTGAGGTGGATATCGGTGGCTCCAAGGTGTCTGTTCTATACCTGGACACCGAAGGATTTGAGAGTGTTGGAAAATC

Basic information

species Zea mays
transcript GRMZM2G030138_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030138_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g08400.1 (Oryza sativa), 3'ss of exon 4
-----gtaaggttggctcacaactatgccgatgtagttt--actattgtaatatctttatcgacggatatcgacaaactgatccacactatacagGTATATGGGTATGGGGTTCCCCCGTTGAGGTGGATATCGGTGGCTCCAAGGTGTCTGTTCTATACCTGGACACCGAAGGATTTGAGAGTGTTGGAAAATC
     ||   |     | |||||| ||   ||||  |    | |  |   ||||| | || || ||||    |||  ||| ||||||   |  |||||||||||| |||||| | ||| ||||| | ||| |   ||||||||| || ||||| || ||||||||||| || |||||||||||  | ||||||||
gtttggtggtgccaa-tgacaactttgt-aatgttatcctaaatgattccatatcctaattgaaggattctaacactctgctccacatattgaagGTATATGGGTCTGGGGTACTCCCATTGAGTTAGATGTGAATGGCTCCAAAGTTTCTGTCCTTTACCTGGACACTGAGGGATTTGAGAGCATCGGAAAATC
















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|76924745|gb|DV170113.1|DV170113
EST:     GTTTTGGAGTTGGACACATGCGGGATACAAAAACAAAAG                         GTATATGGGTATGGGGTTCCCCCGTTGAGGTGGATATCGGTGGCTCCAAGG
genomic: GTTTTGGAGTTGGACACATGCGGGATACAAAAACAAAAGgtaaggttgg ... cactatacagGTATATGGGTATGGGGTTCCCCCGTTGAGGTGGATATCGGTGGCTCCAAGG
EST: gi|89763546|gb|DY690690.1|DY690690
EST:     GTTTTGGAGTTGGACACATGCGGGATACAAAAACAAAAG                         GTATATGGGTATGGGGTTCCCCCGTTGAGGTGGATATCGGTGGCTCCAAGG
genomic: GTTTTGGAGTTGGACACATGCGGGATACAAAAACAAAAGgtaaggttgg ... cactatacagGTATATGGGTATGGGGTTCCCCCGTTGAGGTGGATATCGGTGGCTCCAAGG
EST: gi|71449828|gb|DR830878.1|DR830878
EST:     GTTTTGGAGTTGGACACATGCGGGATACAAAAACAAAAG                         GTATATGGGTATGGGGTTCCCCCGTTGAGGTGGATATCGGTGGCTCCCAGG
genomic: GTTTTGGAGTTGGACACATGCGGGATACAAAAACAAAAGgtaaggttgg ... cactatacagGTATATGGGTATGGGGTTCCCCCGTTGAGGTGGATATCGGTGGCTCCAAGG

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: 11 (upstream exon), 44 (downstream exon)
Score: 4

GTTTTGGAGTTGGACACATGCGGGATACAAAAACAAAAGgtaaggttgg ... cactatacagGTATATGGGTATGGGGTTCCCCCGTTGAGGTGGATATCGGTGGCTCCAAGGTGTCTGTTCTATACCTGGACACCGAAGGATTTGAGAGTGTTGGAAAATC


Block sizes: 39 (upstream exon), 42 (downstream exon)
Score: 2

GTTTTGGAGTTGGACACATGCGGGATACAAAAACAAAAGgtaaggttgg ... cactatacagGTATATGGGTATGGGGTTCCCCCGTTGAGGTGGATATCGGTGGCTCCAAGGTGTCTGTTCTATACCTGGACACCGAAGGATTTGAGAGTGTTGGAAAATC


Block sizes: 19 (upstream exon), 44 (downstream exon)
Score: 5

GTTTTGGAGTTGGACACATGCGGGATACAAAAACAAAAGgtaaggttgg ... cactatacagGTATATGGGTATGGGGTTCCCCCGTTGAGGTGGATATCGGTGGCTCCAAGGTGTCTGTTCTATACCTGGACACCGAAGGATTTGAGAGTGTTGGAAAATC


Block sizes: 39 (upstream exon), 44 (downstream exon)
Score: 15

GTTTTGGAGTTGGACACATGCGGGATACAAAAACAAAAGgtaaggttgg ... cactatacagGTATATGGGTATGGGGTTCCCCCGTTGAGGTGGATATCGGTGGCTCCAAGGTGTCTGTTCTATACCTGGACACCGAAGGATTTGAGAGTGTTGGAAAATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactattgtaatatctttatcgacggatatcgacaaactgatccacactatacagGTATATGGGTATGGGGTTCCCCCGTTGAGGTGGATATCGGTGGCTCCAAGGTGTCTGTTCTATACCTGGACACCGAAGGATTTGAGAGTGTTGGAAAATC
                                   aactgat  putative branch site (score: 15)
     ttgtaatatctttat  TA-rich tract