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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtctataccacctattatcaataattcaatattgcaagttgaaataatttacgggtagtctatcctaactgttgactatgttcagGCAAAAAAATTGCTGCACTGTTTGTCATCCGAACCACTTCGTAGATGGTGCACATATGAGTGGTTCTACAGCGCAGTTGATTATCCATGGTTTTCAAGTA

Basic information

species Zea mays
transcript GRMZM2G395749_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G395749_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g09760.1 (Oryza sativa), 3'ss of exon 10
gtagtctataccacctattatcaataattcaatattgcaagttgaaataatttacgggtagtctatcctaactgttgactatgttcagGCAAAAAAATTGCTGCACTGTTTGTCATCCGAACCACTTCGTAGATGGTGCACATATGAGTGGTTCTACAGCGCAGTTGATTATCCATGGTTTTCAAGTA
|| | ||||| | |||||| | || || |||| | | | ||||||| ||| | | | || ||||||| | | ||||| ||| || |||||||| || |||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||| ||
---gtacac-ccaccattcatcaatgctagtatgccacagattgagttcaact----gtagtct----taattctggcttactttcagGCTAGGAGATTGCAGCATTGCTTGTCATCTGAGTCACTTCGTAGATGGTGTACATATGAGTGGTTTTACAGCGCAGTTGATTATCCATGGTTTATGGATA

upper sequence: GRMZM2G395749_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT3G21430.2 (Arabidopsis thaliana), 3'ss of exon 12
---------------------------------------------------gtagtc-tataccacctattatcaataattcaatattgcaagttgaaataatttacgggt------agtctatcctaactgttgactat-gttcagGCAAAAAAATTGCTGCACTGTTTGTCATCCGAACCACTTCGTAGATGGTGCACATATGAGTGGTTCTACAGCGCAGTTGATTATCCATGGTTT-TCAAGTA--
| ||| || | | | | | || | | | ||| | | | || | | | || | | ||| || | |||| ||| | | || || ||| || | || | | || |||||||| | | ||||||||||||||| ||| |||| |||||||||||| || |
gtgagtgaactttctgatactcagactttattcccaaatgataaagaaaccgcagtgatacatctttcaatcttaagatcttta-atttctatggaatttagtctgtgagttccctgattatatttataccatatcctattattctgcagGAGAAGTTTTCGCATTGCATTTCTAGTTTCCGAGCACGGAGATGGTGTATTTTTGAGTGGTTCTACAGTGCAATTGACTATCCATGGTTTGCCAGACAAG

upper sequence: GRMZM2G395749_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv05s0020g01610.t01 (Vitis vinifera), 3'ss of exon 10
gtagtctataccacctattatcaataattcaatattgcaagttgaaataatttacgggtagtctatcctaactgttgactatgttcagGCAAAAAAATTGCTGCACTGTTTGTCATCCGAACCACTTCGTAGATGGTGCACATATGAGTGGTTCTACAGCGCAGTTGATTATCCATGGTTTTCAAGTA---
|| | | | |||| | ||| ||| || | | ||| | || | | || | | | | | | |||| || || | || | || | | | | | || |||||||| | | ||||||||||||||| ||| ||||||| ||||||||| | | |
---gttaaaattttttgttatgtccatttctataatgtttggttccttaaagtttaaatatttttgtata--tataaattttaattgcagGAAAAGCTTTCTA-ATTGCCTATCTTGCTATCGGGTACGGAGATGGTGTGCTTTTGAGTGGTTCTACAGTGCAATTGATTACCCATGGTTTGCTAAAAAGG

upper sequence: GRMZM2G395749_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv14s0128g00880.t01 (Vitis vinifera), 3'ss of exon 2
gtagtctataccacctattatcaataattcaatattgcaagtt------gaaataatttacgggtagtctatcctaactgttg-actatgttcagGCAAAAAAATTGCTGCACTGTTTGTCATCCGAACCACTTCGTAGATGGTGCACATATGAGTGGTTCTACAGCGCAGTTGATTATCCATGGTTT-TCAAGTA--
|| | | | | | || ||| | |||| | |||| || |||| || | | || | | || ||| | || || || ||| || | || ||||| | |||||||||||||| | |||||||||||||| ||| ||||||| || |||||| | || |
gttgaatttgc-atcttccttcactttttcagaaacttcagttatctaagatataaaataaagctgacataaattgtttttttcactgtatttgtagAAGAAGATTTCT-TGTTCCTTATCATCTTACATGGCACGTAGATGGTGCACTTTCGAGTGGTTCTACAGTGCAATTGATTACCCTTGGTTTGTTAAAAAAG

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|31354962|gb|CD439319.1|CD439319
EST:     ATTGCAAAACAAAGCATATGTCATGCAATGAAGGTTCAGATAATTTACAG                         GCNNNNNNNTTGCTGCACTGTTTGTCATCCGAACCACTTCGTAGATGGTGC
genomic: ATTGCAAAACAAAGCATATGTCATGCAATGAAGGTTCAGATAATTTACAGgtagtctata ... ctatgttcagGCAAAAAAATTGCTGCACTGTTTGTCATCCGAACCACTTCGTAGATGGTGC




















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 3 RNA-Seq libraries.


Block sizes: 27 (upstream exon), 48 (downstream exon)
Score: 3

CAAGCCTGAAGTGAGAATGTCTGGAAGGACCAGACGGAAATCTCAAATGCATTGCAAAACAAAGCATATGTCATGCAATGAAGGTTCAGATAATTTACAGgtagtctata ... ctatgttcagGCAAAAAAATTGCTGCACTGTTTGTCATCCGAACCACTTCGTAGATGGTGCACATATGAGTGGTTCTACAGCGCAGTTGATTATCCATGGTTTTCAAGTA


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 13

CAAGCCTGAAGTGAGAATGTCTGGAAGGACCAGACGGAAATCTCAAATGCATTGCAAAACAAAGCATATGTCATGCAATGAAGGTTCAGATAATTTACAGgtagtctata ... ctatgttcagGCAAAAAAATTGCTGCACTGTTTGTCATCCGAACCACTTCGTAGATGGTGCACATATGAGTGGTTCTACAGCGCAGTTGATTATCCATGGTTTTCAAGTA


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 13

CAAGCCTGAAGTGAGAATGTCTGGAAGGACCAGACGGAAATCTCAAATGCATTGCAAAACAAAGCATATGTCATGCAATGAAGGTTCAGATAATTTACAGgtagtctata ... ctatgttcagGCAAAAAAATTGCTGCACTGTTTGTCATCCGAACCACTTCGTAGATGGTGCACATATGAGTGGTTCTACAGCGCAGTTGATTATCCATGGTTTTCAAGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcaagttgaaataatttacgggtagtctatcctaactgttgactatgttcagGCAAAAAAATTGCTGCACTGTTTGTCATCCGAACCACTTCGTAGATGGTGCACATATGAGTGGTTCTACAGCGCAGTTGATTATCCATGGTTTTCAAGTA
     aagttgaaataattta  TA-rich tract