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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtcatcctgtttccttcctgatgatgtgctttggtgtaatgcaatgcaatgctgcctgggctgacggcttttctctgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGA

Basic information

species Zea mays
transcript GRMZM2G437859_T04
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G437859_T04 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g55500.2 (Oryza sativa), 3'ss of exon 11
gttggtcatcctgtttccttcctgatgatgtgctttggtgtaatgcaatgcaatgctgcctgggctgacggcttttctctgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGA
|||||| | ||||   | |  ||||||  | |       |  |     |    |  || ||         |||||  | ||||| ||||| || |||||||| |||||| | ||||| |||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| || || || ||
gttggttaccctgcgccat--ctgatg-cgagtaaatacgccactgtttttgttcttgtctcacacatttgctttgtt-tgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGTGTCTCCATCTTTCTTGGCCTATCTGTGCCCGA

upper sequence: GRMZM2G437859_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G12360.1 (Glycine max), 3'ss of exon 13
----------------------gttggtcatcctgtttc-cttcctgatgatgtgctttggtgtaatgcaatgcaatgctgc-ctgggctgacggcttttctctgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGA
                        |    | |    |   | |  | || || |    |  | | || |  |    |||     |  |   |  |||  | |     |  ||||| | ||||||||||| ||  |||||||||||||||||||||| ||| | |||||||||||    ||||| ||| ||||| | ||  ||||| | || ||
gtgagtaccaccaactaaactaactaactaactaactaagcctttttattatatatacta-tttgattccttcttctgccttgttatgacaattgctaattttgtttttgcagCTTCTGTGGGGCTGTCATTTTTACAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTTGTGGCGTTTCCCTCTTCTTAGGTTTGTCCATTCCTGA

upper sequence: GRMZM2G437859_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA06G06840.1 (Glycine max), 3'ss of exon 11
gttggtcatcctgtttccttcctgatgatgtgctttggtgtaatgcaatgcaatgctgcctgggctgacggcttttctctgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGA
||  ||    |  ||||     || |   ||       |||  |    | |  |      |    ||||   |||||||| | |  ||||| | |||||||| || ||| | |||||||||||||||||||| ||| | |||||||||||  | || ||  || | ||| | ||  | || || || ||
gtgagtatcaccatttcacctatggtttagtttaagcatgtctttgcttcctctatctttttta-tgacaa-ttttctct-atttgcagCTTCTGTGGGGCTATCATTCTTGCAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTCTTGGTGTAGCCCTTTTCTTAGGTTTTTCTGTTCCTGA

upper sequence: GRMZM2G437859_T04 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA04G06750.1 (Glycine max), 3'ss of exon 11
gttggtcatcctgtttccttcctgatgatgtgctttggtgtaatgcaatgcaatgctgcctggg-ctgacggcttttctctgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGA
||  ||    |   |||  |||||  | |  | ||     |            |    | |    || ||    ||  | |   |  ||||| | |||||||| || ||| | |||||||||||||||||||| ||| | ||||||||||| || || ||  || | ||| | ||  | || || || ||
gtgagtatcaccacttc--tcctgtggtttagtttaaacatctctttgcttcctctatcttatttctaacaagcttatttt--tttgcagCTTCTGTGGGGCTATCATTCTTGCAGTTCACTAACATGAACTCAATGAGGAACCTCTTTATTGTTGGTGTTGCCCTTTTCTTAGGTTTTTCTGTTCCTGA

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|91049744|gb|EB160162.1|EB160162
EST:     CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG                         CTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA
genomic: CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTGgttggtcatc ... tgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA
EST: gi|149071735|gb|EE160128.2|EE160128
EST:     CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG                         CTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA
genomic: CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTGgttggtcatc ... tgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA
EST: gi|71759661|gb|DR957598.1|DR957598
EST:     CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG                         CTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA
genomic: CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTGgttggtcatc ... tgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA
EST: gi|50337438|gb|CO532564.1|CO532564
EST:     CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG                         CTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA
genomic: CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTGgttggtcatc ... tgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA
EST: gi|50337437|gb|CO532563.1|CO532563
EST:     CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG                         CTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA
genomic: CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTGgttggtcatc ... tgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA
EST: gi|211379070|gb|FL028411.1|FL028411
EST:     CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG                         CTGCGGTGGGGCTGTC
genomic: CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTGgttggtcatc ... tgactctcagCTGCGGTGGGGCTGTC
EST: gi|76287139|gb|DV026707.1|DV026707
EST:     CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG                         CTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA
genomic: CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTGgttggtcatc ... tgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA
EST: gi|76287138|gb|DV026706.1|DV026706
EST:     CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG                         CTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA
genomic: CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTGgttggtcatc ... tgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA
EST: gi|71310985|gb|DR791794.1|DR791794
EST:     CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTG                         CTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA
genomic: CCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTGgttggtcatc ... tgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCA

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), 48 (downstream exon)
Score: 244

GGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTGgttggtcatc ... tgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 37

GGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTGgttggtcatc ... tgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGA


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 9

GGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTGgttggtcatc ... tgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGA


Block sizes: 47 (upstream exon), 35 (downstream exon)
Score: 11

GGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTGgttggtcatc ... tgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtgtaatgcaatgcaatgctgcctgggctgacggcttttctctgactctcagCTGCGGTGGGGCTGTCCTTCCTACAGTTCACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGA
                                          ctctgac  putative branch site (score: 11)
                                     cttttctctgactctc  CT-rich tract