Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgataatttgctggacatgcatctgtaaatgtttttttaacacattgagatgacataacagttgattggtactactgaatcacttgatctaaccgttcgtcgttgttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCTTACAGAGGTCACTACACTGCTCATGCAAAGCATGCCGACGGGCAATGGC

Basic information

species Zea mays
transcript GRMZM2G327635_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G327635_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g46660.1 (Oryza sativa), 3'ss of exon 6
gtgataatttgctggacatgcatctgtaaatgtttttttaacacattgagatgacataacagttgattggtactactgaatcacttgatctaaccgttcgtcgttgttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCTTACAGAGGTCACTACACTGCTCATGCAAAGCATGCCGACGGGCAATGGC
  |  |    | |        |  |   ||  |  | || |    ||||||  |  | ||  ||  |    |    | ||  |   ||||||||   | |   |      || ||| |||||| |||||||||||||||||||||||| |||| ||||    |||| | ||| || || ||||||||  ||||||||  ||||   |         
--ggaatcacgatcatttcttagtttccaacatgctattgaat--ttgagacaaattgacgcttcttcaa-atagttaaa--atgggatctaacaacttgatttcagCACATGCAGAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGGGCAAACCCGTCCAGGGGCCATTACACTGCCGATGCAAAGTCTGCCAGTG---------

upper sequence: GRMZM2G327635_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g46660.2 (Oryza sativa), 3'ss of exon 6
gtgataatttgctggacatgcatctgtaaatgtttttttaacacattgagatgacataacagttgattggtactactgaatcacttgatctaaccgttcgtcgttgttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCTTACAGAGGTCACTACACTGCTCATGCAAAGCATGCCGACGGGCAATGGC
   || ||||  | |      |  ||  | ||  |||   ||| |||||     | |  ||  |  ||   |              ||||||||   | |   |      || ||| |||||| |||||||||||||||||||||||| |||| ||||    |||| | ||| || || ||||||||  ||||||||  ||||   ||||| ||||
---atcatttcttagtttccaacatgctattgaatttgagacaaattgacgcttctt--caaatagttaaaatgg-----------gatctaacaacttgatttcagcacatgcagAGTAGAAGATATGAGCTTGTTGCAACCATCACGCATCTTGGGGCAAACCCGTCCAGGGGCCATTACACTGCCGATGCAAAGTCTGCCAGTGGGCAGTGGC
















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|5607660|gb|AI901327.1|AI901327
EST:     ATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAG                         GGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
genomic: ATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
EST: gi|211106195|gb|FL465693.1|FL465693
EST:     CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAG                         GGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
genomic: CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
EST: gi|31356664|gb|CD441021.1|CD441021
EST:     CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAG                         GGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
genomic: CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
EST: gi|211500498|gb|FL437355.1|FL437355
EST:     CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAG                         GGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
genomic: CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
EST: gi|60291773|gb|DN190012.1|DN190012
EST:     CTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAG                         GGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
genomic: CTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
EST: gi|24773487|gb|CA408741.1|CA408741
EST:     CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAG                         GGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
genomic: CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
EST: gi|24934826|gb|CA453044.1|CA453044
EST:     CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAG                         GGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
genomic: CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
EST: gi|60346943|gb|DN213916.1|DN213916
EST:     CATCTGAACTGGTTTTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAG                         GGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
genomic: CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
EST: gi|211106194|gb|FL465692.1|FL465692
EST:     CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAG                         GGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
genomic: CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
EST: gi|24764781|gb|CA399943.1|CA399943
EST:     CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAG                         GGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
genomic: CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
EST: gi|5055505|gb|AI734392.1|AI734392
EST:     TAGTCGTGATCTGCTGAGCTCACCATCACAAGAG                         GGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
genomic: TAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
EST: gi|71441837|gb|DR822887.1|DR822887
EST:     CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAG                         GGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
genomic: CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
EST: gi|16917273|gb|BM073212.1|BM073212
EST:     CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAG                         GGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT
genomic: CATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCT

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: 298

CAGTTATGGAAATAATGGGAGCACTAAAATCTACAAGCCACTCGGCTTCACATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCTTACAGAGGTCACTACACTGCTCATGCAAAGCATGCCGACGGGCAATGGC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 104

CAGTTATGGAAATAATGGGAGCACTAAAATCTACAAGCCACTCGGCTTCACATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCTTACAGAGGTCACTACACTGCTCATGCAAAGCATGCCGACGGGCAATGGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 149

CAGTTATGGAAATAATGGGAGCACTAAAATCTACAAGCCACTCGGCTTCACATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCTTACAGAGGTCACTACACTGCTCATGCAAAGCATGCCGACGGGCAATGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

CAGTTATGGAAATAATGGGAGCACTAAAATCTACAAGCCACTCGGCTTCACATCTGAACTGGTTCTTAGTCGTGATCTGCTGAGCTCACCATCACAAGAGgtgataattt ... ttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCTTACAGAGGTCACTACACTGCTCATGCAAAGCATGCCGACGGGCAATGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgattggtactactgaatcacttgatctaaccgttcgtcgttgttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCTTACAGAGGTCACTACACTGCTCATGCAAAGCATGCCGACGGGCAATGGC
                          atctaac  putative branch site (score: 157)
                                             ttgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgataatttgctggacatgcatctgtaaatgtttttttaacacattgagatgacataacagttgattggtactactgaatcacttgatctaaccgttcgtcgttgttgtatacagGGTAGAAAATATGAGCTTGTTGCAACCATCACTCATCATGGGAGGGACCCTTACAGAGGTCACTACACTGCTCATGCAAAGCATGCCGACGGGCAATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG