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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaccatttctttgcctggtttactttggatacagcttgctttcccgtgactgagaaagaagtacatgtgactttgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTCAAGGGGGCATAGGCTAGGTTGTGTTTTGTGTTCTAGAAGAAGAGATAGA

Basic information

species Zea mays
transcript GRMZM2G451366_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G451366_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os08g01180.1 (Oryza sativa), 3'ss of exon 13
gtatggaccatttctttgcctggtttactttggatacagcttgctttcccgtgactgagaaagaagtacatgtgactttgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTCAAGGGGGCATA---GGCTAGGTTGTGTTTTGTGTTCTAGAAGAAGAGATAGA
||||| | ||||||   ||||   | |  |   | ||||   |||||    |  |||     ||     |  |   ||| ||   |||||| | || || ||||| |||||||||||||| || || ||||||||  |||||||||||||   |  ||| ||||| |||||||  ||| |     ||    
gtatgtatcatttcaa-gcct---tcaaatataagacaggaagctttgtttttcctgcagttgaga---acttattttttttaatcagGGTCTTGATGATCTCATCAACATATTCCGGCGACCACCATCACGCAAGGTCAAGGGGGCATAATAGAATAGATTGTGCTTTGTGTATTAGTATCCAGGAA---
















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|76931447|gb|DV172728.1|DV172728
EST:     TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
EST: gi|60354551|gb|DN221524.1|DN221524
EST:     TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
EST: gi|8551643|gb|BE128814.1|BE128814
EST:     TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTAACATATTC
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTC
EST: gi|32809380|gb|CD961614.1|CD961614
EST:     TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTC
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTC
EST: gi|71440388|gb|DR821438.1|DR821438
EST:     TGGGTTCCTACCTGATCGTTCTTTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
EST: gi|148934011|gb|EC878016.2|EC878016
EST:     TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
EST: gi|149109482|gb|EE293326.2|EE293326
EST:     TGGGTTCCTACCTGATCGTTCTTTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
EST: gi|60356118|gb|DN223091.1|DN223091
EST:     TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
EST: gi|17930706|gb|BM267666.1|BM267666
EST:     TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
EST: gi|78123288|gb|DV541672.1|DV541672
EST:     TGGGTTCCTACCTGATCGTTCTTTTTTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
EST: gi|60347494|gb|DN214467.1|DN214467
EST:     TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
EST: gi|32826642|gb|CD966320.1|CD966320
EST:     TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTA
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTA
EST: gi|71326873|gb|DR800095.1|DR800095
EST:     TGGGTTCCTACCTGATCGTTCTTTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
EST: gi|32827213|gb|CD966891.1|CD966891
EST:     TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTA
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTA
EST: gi|211499697|gb|FL406840.1|FL406840
EST:     TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
EST: gi|32936202|gb|CF041014.1|CF041014
EST:     TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
EST: gi|32794438|gb|CD946674.1|CD946674
EST:     TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTA
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTA
EST: gi|60357371|gb|DN224344.1|DN224344
EST:     TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGG                         GGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC
genomic: TGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTC

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: 39 (upstream exon), 42 (downstream exon)
Score: 25

GTTGCAAGTGTTACCTTTGATCTGCTGTTCCTTCTGGTGCTGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTCAAGGGGGCATAGGCTAGGTTGTGTTTTGTGTTCTAGAAGAAGAGATAGA


Block sizes: 47 (upstream exon), 35 (downstream exon)
Score: 41

GTTGCAAGTGTTACCTTTGATCTGCTGTTCCTTCTGGTGCTGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTCAAGGGGGCATAGGCTAGGTTGTGTTTTGTGTTCTAGAAGAAGAGATAGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 29

GTTGCAAGTGTTACCTTTGATCTGCTGTTCCTTCTGGTGCTGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTCAAGGGGGCATAGGCTAGGTTGTGTTTTGTGTTCTAGAAGAAGAGATAGA


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 21

GTTGCAAGTGTTACCTTTGATCTGCTGTTCCTTCTGGTGCTGGGTTCCTACCTGATCGTTCTCTTCTGTTTCCTAGTAATCAGTACACGGgtatggacca ... tgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTCAAGGGGGCATAGGCTAGGTTGTGTTTTGTGTTCTAGAAGAAGAGATAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacagcttgctttcccgtgactgagaaagaagtacatgtgactttgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTCAAGGGGGCATAGGCTAGGTTGTGTTTTGTGTTCTAGAAGAAGAGATAGA
                                          ctttgtt  CT-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggaccatttctttgcctggtttactttggatacagcttgctttcccgtgactgagaaagaagtacatgtgactttgttgggcagGGTGTCGACGACCTCATTAACATATTCCGGCGGCCTCCGTCACGCAAACTCAAGGGGGCATAGGCTAGGTTGTGTTTTGTGTTCTAGAAGAAGAGATAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA