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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgacttttgtttagatttggcttcccttcaattggttaaccgtgaataagcccgctaacctgatgattcctagctacatatcctggcggcagtgagaaactgtctgccgccaaagccctcaacagttttttttagttttgctaagcctttttttttgcatgtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGAAGAGATGAAGGCAGTTGCAGAGTACATTAGGAAGCAAGGGAGAGT

Basic information

species Zea mays
transcript GRMZM2G179429_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179429_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g01320.1 (Oryza sativa), 3'ss of exon 7
gtatgtgacttttgtttagatttggcttcccttcaattggttaaccgtgaataagcccgctaacctgatgattcctagctacatatcctggcggcagtgagaaactgtctgccgccaaagccctcaacagttttttttagttttgctaagcctttttttttgcatgtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGAAGAGATGAAGGCAGTTGCAGAGTACATTAGGAAGCAAGGGAGAGT
||||||  |  |  |||     | |   |  ||   |||    || |   || ||||       |  ||| ||      | |||||  ||||             || ||   |  ||    |||  ||   || ||| || | | |  ||     |||    |    || ||||||||| ||||||| || |||||||| |||||||||||||| ||||| || ||||| ||||||||||| || ||||| ||||| ||||| |||||||| ||
gtatgtatcactcttttgtgacttgaaactattgtcttgtgctactgc--atcagcctaagtggcatatgctt------tgcatattttggca------------tgact--tgataagttactccgcaaccttgtttggtct-gatgggctgcccttt----acaataccacagATAGGCTATCTGGTGTCATGGATGATCGTGGGAAGTTCATATACATATCTACTGAGGAGATGAAGGCTGTCGCAGATTACATCAGGAAACAAGGGAGGGT
















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|88754687|gb|DY538828.1|DY538828
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG                         ATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
EST: gi|31364620|gb|CD448975.1|CD448975
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG                         ATAGGTTATCTGGTGTGATGGATGACCGTGGGAAGTTCATCTACATC
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATC
EST: gi|71773570|gb|DR971468.1|DR971468
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG                         ATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
EST: gi|94472565|gb|EB701523.1|EB701523
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG                         ATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
EST: gi|71307150|gb|DR789746.1|DR789746
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG                         ATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
EST: gi|91048409|gb|EB158827.1|EB158827
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG                         ATAGGTTATCTGGGGGTGATGGATGACCG
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGG-TGATGGATGACCG
EST: gi|211427421|gb|FL445183.1|FL445183
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG                         ATAGGTTATCTGGTGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
EST: gi|4688549|gb|AI637219.1|AI637219
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG                         ATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
EST: gi|148958245|gb|EC904458.2|EC904458
EST:     GACTGTATNCA-TCGGATTGTTACTCTGGAAAGCATGG                         ATAGGTTATCTGGGGTGATGGATGACCGTGG
genomic: GACTGTAT-CAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGG
EST: gi|211469382|gb|FL187167.1|FL187167
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG                         ATAGGTTATCTGGTGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
EST: gi|31364129|gb|CD448484.1|CD448484
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG                         ATAGGTTATCTGGTGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
EST: gi|32165071|gb|CD670389.1|CD670389
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG                         ATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
EST: gi|60357983|gb|DN224956.1|DN224956
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG                         ATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
EST: gi|148932548|gb|EC876363.2|EC876363
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG                         ATAGGTTATCTGGTGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
EST: gi|78112541|gb|DV530935.1|DV530935
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG                         ATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCA

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: 37 (upstream exon), 45 (downstream exon)
Score: 123

GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGAAGAGATGAAGGCAGTTGCAGAGTACATTAGGAAGCAAGGGAGAGT


Block sizes: 37 (upstream exon), 48 (downstream exon)
Score: 126

GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGAAGAGATGAAGGCAGTTGCAGAGTACATTAGGAAGCAAGGGAGAGT


Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 155

GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGAAGAGATGAAGGCAGTTGCAGAGTACATTAGGAAGCAAGGGAGAGT


Block sizes: 37 (upstream exon), 46 (downstream exon)
Score: 147

GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGgtatgtgact ... gtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGAAGAGATGAAGGCAGTTGCAGAGTACATTAGGAAGCAAGGGAGAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctcaacagttttttttagttttgctaagcctttttttttgcatgtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGAAGAGATGAAGGCAGTTGCAGAGTACATTAGGAAGCAAGGGAGAGT
                                           atgtaac  putative branch site (score: 147)
        agttttttttagtttt  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgacttttgtttagatttggcttcccttcaattggttaaccgtgaataagcccgctaacctgatgattcctagctacatatcctggcggcagtgagaaactgtctgccgccaaagccctcaacagttttttttagttttgctaagcctttttttttgcatgtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGAAGAGATGAAGGCAGTTGCAGAGTACATTAGGAAGCAAGGGAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG