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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAGGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttatttaatttgggcatgctttatgtcttttttttttctatccagagtttgcgtaaatctttgttccttgccctttacag

Basic information

species Zea mays
transcript GRMZM2G032267_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 5'ss of exon 9
AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAGGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttatttaatttgggcatgctttatgtcttttttttttctatccagagtttgcgtaaatctttgttccttgccctttacag
|||||| |||||||| |||||||||||||||||||| || |||||||| || |||||||||||||| |||||||||||||| || ||||||||||| ||||||      | |||| || ||  | |||  |||    ||| || |  |||  |    |  ||||||| || ||| ||| |||||
AGGAACTGATATGACAAGTCCACATGGTATACCAGTTGATCTTCTAGACAGATTGGTGATTATTCGAACAGAAACATATGGTCCCACTGAGATGATCCAGgtt------tgattttgg-atcttatatcacttaggctttcctgtttagaaatgtgtttgatctttgctcattgtcctctacag

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 5'ss of exon 9
AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAGGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttatttaatttgggcatgctttatgtcttttttttttctatccagagtttgcgtaaatctttgttccttgccctttacag
|||||| |||||||| ||||| |||||||||||||| || ||||||||| | |||||||||||||| ||||||||||| || || ||||||||||| ||||||    |||   |     ||   ||| |   ||||| | ||||     | | || || | |||| | || | ||| ||| |||
AGGAACTGATATGACAAGTCCGCATGGTATACCAGTTGATCTTCTAGATCGATTGGTGATTATTCGAACAGAAACATACGGTCCCACTGAGATGATCCAGgtttgattttgggtcttatatcagttaggc--tttttctgtcta---gaaatgtgtgtgattctt-gctcatcgccgtttgcag

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G21830.1 (Glycine max), 5'ss of exon 9
AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAGGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgt----------tcttatttaatttgggcatgctttatgtcttttttttttctat-ccagagtttgcgtaaatctttgttccttgcccttt--acag
|||||| |||||||| ||||| ||||| ||||| || |||||  | ||| |||||||||| ||||| ||  |||||||||| ||| |||| |||||||||||          || | |||  ||     |   || |     ||     || | |    |  | | |  | ||   || | |||     |   ||||
AGGAACTGATATGACAAGTCCTCATGGCATACCTGTTGACCTGTTGGATCGGTTGGTGATCATTCGAACGCAAACATATGGTCCTGCTGAAATGATACAGgtagtatggccttcatctttctttcaaatagatttcaaaatgttaagcattatgtgtttggatatacaaacatacatgcttcttaattgtgggacag

upper sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA07G02170.1 (Glycine max), 5'ss of exon 9
AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAGGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgt----------tcttatttaatttgggcatgctttatgtcttttttttttctat-ccagagtttgcgtaaatctttgttccttgcccttt--acag
||| || |||||||| ||||| ||||| ||||| || |||||  | ||| |||||||||| ||||| ||  |||| ||||| ||| |||| |||||||||||          || | | |  ||||   |   || |      | | | || | |    |  | | |  | ||   || | |||     |   ||||
AGGGACTGATATGACCAGTCCTCATGGCATACCTGTTGACCTGTTGGATCGGTTGGTGATCATTCGAACGCAAACCTATGGTCCTGCTGAAATGATACAGgtagtatggctttcatgtgtcttttgaatagatttcaaaatgctatgtcttatgtgtttggatatacaaacatacatgcttcttaattgtggaacag

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|32932061|gb|CF036873.1|CF036873
EST:     GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATATTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|60342617|gb|DN209590.1|DN209590
EST:     GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|4314889|gb|AI444686.2|AI444686
EST:     GG-TGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|4826086|gb|AI667714.1|AI667714
EST:     GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|32842037|gb|CD981718.1|CD981718
EST:     GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATATTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|21331671|gb|BQ487052.1|BQ487052
EST:     GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|60358619|gb|DN225592.1|DN225592
EST:     GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|60347035|gb|DN214008.1|DN214008
EST:     GGTTGGTGATTATTCGGACAGAAACATATGCCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|22819003|gb|BU499093.1|BU499093
EST:     GGGTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|87157723|gb|DY402512.1|DY402512
EST:     GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|26559755|gb|CA831990.1|CA831990
EST:     GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|33096873|gb|CF056833.1|CF056833
EST:     GGTTGGTGATTATTCGGACAGAGACATATGGCCCTACTGAGATGATACAG                         ATATTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|32840485|gb|CD980166.1|CD980166
EST:     GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATATTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|60356915|gb|DN223888.1|DN223888
EST:     GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|4321073|gb|AI467736.1|AI467736
EST:     GGTTGGTGATTATTCGG-CAGAAACATATGGCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|67016264|gb|CO445013.1|CO445013
EST:     GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|148952636|gb|EC898467.2|EC898467
EST:     GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|32842224|gb|CD981905.1|CD981905
EST:     GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATATTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|7227451|gb|AW566092.1|AW566092
EST:     GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
EST: gi|71420713|gb|DR805175.1|DR805175
EST:     GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAG                         ATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT
genomic: GGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGT

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: 56

AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAGGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 18

AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAGGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 22

AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAGGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 24

AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAGGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttattt ... ccctttacagATACTGGCTATCCGAGCACAAGTGGAAGAGATTGATATCGATGAAGAAAGTCTTGCTTATTTAGGCGAGATCGGACAGCAGACATCTTTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAACCGATATGACGAGTCCACATGGTATACCAGTGGACCTTCTAGATAGGTTGGTGATTATTCGGACAGAAACATATGGCCCTACTGAGATGATACAGgttcttatttaatttgggcatgctttatgtcttttttttttctatccagagtttgcgtaaatctttgttccttgccctttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG