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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgacgtcaaacaaagcacacatgtagtcttgggtttttatgacccatttttcttatcgattaattattcttatgactattgttttcaatgtttatcagGTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACC

Basic information

species Zea mays
transcript GRMZM2G094699_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G392003_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g07280.1 (Oryza sativa), 3'ss of exon 2
-------gttgacgtcaaacaaa-gcacacatgtagtcttgggtttttatgacccatttttcttatcgattaattattcttatgactattgttttcaatgtttatcagGTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACC
       ||||  ||| |      |    |||||    |||    | ||| ||  || ||| |    |  | | |||   ||| | ||||   ||    ||| || ||||||| ||||| ||||| || ||||||||||||||||| ||| ||||||| || || || ||||| ||||||||||||||||||||
tatgctggttgttgtcgatttgttgtgatcatgtccatttgttaatgtataactgatcttttt----ggcttaatatgactattattatttcctt----gttcattagGTGGCTGTGAACACTGTCATTCAGGATGAGAAGGAATTTTTGGATCATATCATCAAATCGACAAATATGAAGTGTCTAACACCACC

upper sequence: GRMZM2G392003_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g07280.2 (Oryza sativa), 3'ss of exon 2
-------gttgacgtcaaac-aaagcacacatgtagtcttgggtttttatgacccatttttcttatcgattaattattcttatgactattgttttcaatgtttatcagGTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACC--------------
       ||||  ||| |      |    |||||    |||    | ||| ||  || ||| |    |  | | |||   ||| | ||||   ||    ||| || ||||||| ||||| ||||| || ||||||||||||||||| ||| ||||||| || || || ||||| ||||||||||||||||||||              
tatgctggttgttgtcgatttgttgtgatcatgtccatttgttaatgtataactgatcttttt----ggcttaatatgactattattatttcctt----gttcattagGTGGCTGTGAACACTGTCATTCAGGATGAGAAGGAATTTTTGGATCATATCATCAAATCGACAAATATGAAGTGTCTAACACCACCGTAAGTTACAATGA
















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|16377392|gb|BI991902.1|BI991902
EST:     CTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAG                         GTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATT
genomic: CTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAGgtaatagacc ... tgtttatcagGTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATT
EST: gi|148934854|gb|EC878899.2|EC878899
EST:     CTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAG                         GTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATT
genomic: CTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAGgtaatagacc ... tgtttatcagGTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATT
EST: gi|6012725|gb|AW062162.1|AW062162
EST:     CTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAG                         GTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATT
genomic: CTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAGgtaatagacc ... tgtttatcagGTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATT
EST: gi|67015126|gb|CO443875.1|CO443875
EST:     CTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAG                         GTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATT
genomic: CTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAGgtaatagacc ... tgtttatcagGTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATT
EST: gi|71764263|gb|DR962200.1|DR962200
EST:     GTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAG                         GTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATT
genomic: GTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAGgtaatagacc ... tgtttatcagGTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATT
EST: gi|12967981|gb|BG264928.1|BG264928
EST:     CTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAG                         GTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATT
genomic: CTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAGgtaatagacc ... tgtttatcagGTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATT
EST: gi|67011141|gb|CO439890.1|CO439890
EST:     CTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAG                         GTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATT
genomic: CTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAGgtaatagacc ... tgtttatcagGTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATT

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), 40 (downstream exon)
Score: 105

AAATGACATTCACATTGATATTATGGATTACATCTCACCTGCTACATGTGCTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAGgtaatagacc ... tgtttatcagGTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 73

AAATGACATTCACATTGATATTATGGATTACATCTCACCTGCTACATGTGCTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAGgtaatagacc ... tgtttatcagGTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 103

AAATGACATTCACATTGATATTATGGATTACATCTCACCTGCTACATGTGCTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAGgtaatagacc ... tgtttatcagGTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 158

AAATGACATTCACATTGATATTATGGATTACATCTCACCTGCTACATGTGCTGATGTTGCATTCCGGAACATGTGGGCAGAATTTGAGTGGGAAAATAAGgtaatagacc ... tgtttatcagGTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatttttcttatcgattaattattcttatgactattgttttcaatgtttatcagGTGGCGGTGAATACTGTGATCCAGGATGAGAAGGAATTCTTGAATCATATTATTAAGTCCACAAACATGAAGTGTCTAACACCACC
              gattaat  putative branch site (score: 158)
               attaattattcttatg  TA-rich tract