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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcactggctatatctcttgtcaacttgttgcacacttgttcatgtggtaccgtgcacactcattttattatttgggtatgtagGGAGAGCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTTGAACCCCTTAGGAATCGTCTCTCTGAGAACACTGAACTACAAAGTGCTA

Basic information

species Zea mays
transcript GRMZM2G032351_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032351_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g23890.4 (Oryza sativa), 3'ss of exon 8
-------------------------gtactcactggctatatctcttgtcaacttgttgcacacttgttcatgtggt-accgtgca-cactcattttattatttgggtatgtagGGAGAGCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTTGAACCCCTTAGGAATCGTCTCTCTGAGAACACTGAACTACAAAGTGCTA
                          ||||| |  |   | |      |  | || ||    | | ||   | || | ||        | | |||  |  || || |  || |||| |||||||||||||||||||| || ||| | |||||||| || |||||||||||||| ||||| || || || ||||| |||||  |||| ||||| |
gtatctgaaaaatctgtgccaaatgctactcccaagtattttggagcttgcaatttttaactagtagtgggtatgattactacatggtagtgattgcac-atctgtgagtgcagGGGGAGCTTCAATACTTCATTGGTGTGCAACTTGATGGAAGTGATCATGTTGAACCCCTCAGGAACCGCCTTTCGGAGAATACTGAGATACAGAGTGCCA

upper sequence: GRMZM2G032351_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G33560.1 (Glycine max), 3'ss of exon 8
-----------------------------------------gtactcactggctatatctcttgt-caacttgttgcacacttgttcatgtggtaccgtgcacactcattttattatttgggtatgtagGGAGAGCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTTGAACCCCTTAGGAATCGTCTCTCTGAGAACACTGAACTACAAAGTGCTA
                                           |   ||   | |||||| ||   |||    |||    |       | | ||  |        |   |  || |||||  ||| ||||| || ||||||||||||||||| |||||| | |||||||| || ||||| |||||| | |  || || || |||||||  ||||| | |||||||||||
gtgaatgtgatactgttatggtagaaaacaattaatctgaatcatgaacattcaatatctattaaacaatacattgtgttcccccctttttagtttctaatgt-ttttctcaatgatttg--tatttagGGTGAACTTCAATACTTCATTGGTGTTCAACTAGATGGAAGTGATCATGTAGAACCCTTAAAAAACCGCCTGTCTGAGACAACTGAGCAACAAAGTGCTA

upper sequence: GRMZM2G032351_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA16G19560.1 (Glycine max), 3'ss of exon 10
--------------------------------------gtactcactggctatatctcttgtcaacttgttgcacacttgttcatgtggtaccgtgcacactcatttt--attatttgggtatgtagGGAGAGCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTTGAACCCCTTAGGAATCGTCTCTCTGAGAACACTGAACTACAAAGTGCTA
                                      | ||  |     |  || |||  | ||||   |     |||   |   |  ||   |  |   | ||| |  || |||||  ||| ||||| || ||||||||||||||||| |||||| | |||||||| || ||||| |||||| | |  || || || |||||||  ||||| | |||||||||||
gtgaaagtgatactgttatgctagaaaacaaataatttgaacataaacattcaatatctattaaactatatattgtcttcccccctttctagtttctaatgttattctcaatgatttg--tatttagGGTGAACTTCAATACTTCATTGGTGTTCAACTAGATGGAAGTGATCATGTAGAACCCTTAAAAAACCGCCTGTCTGAGACAACTGAGCAACAAAGTGCTA

upper sequence: GRMZM2G032351_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv03s0038g04210.t01 (Vitis vinifera), 3'ss of exon 8
-----------gtactcactggctatatctcttgtcaacttgttgcac-------acttgttcatgtggtaccgtgcacactcatttt---attatttgggtat----gtagGGAGAGCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTTGAACCCCTTAGGAATCGTCTCTCTGAGAACACTGAACTACAAAGTGCTA
            |||| | |   |||| |||||       | ||| |        |  | || |||  | | | | |    | | |||   | | |   | |||    |||||| || ||||||||||||||||| || ||||| |||||||| || ||| | ||||||||  | || || || || ||| | ||||| | |||||||||||
gtggctatgagatacttattctatataactcttaatttggttttggatgaagagaatgtatttatgctgcagcttccttcatgactttccaagtctcctgttatattcgtagGGTGAACTTCAATACTTCATTGGTGTCCAATTAGATGGAAGTGATCATCTGGAACCCCTCCGAAACCGCCTGTCAGAGCAAACTGAGCAACAAAGTGCTA

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|71434885|gb|DR815935.1|DR815935
EST:     GGAAGAAGTTTTGGAACTTGTTCCACCTACAGCCAATGCGAGACCAGAAA                         GGAGAGCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTT
genomic: GGAAGAAGTTTTGGAACTTGTTCCACCTACAGCCAATGCGAGACCAGAAAgtactcactg ... gggtatgtagGGAGAGCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTT
EST: gi|32850736|gb|CD990417.1|CD990417
EST:     GGAAGAAGTTTTGGAACTTGTTCCACCTACAGCCAATGCGAGACCAGAAA                         GGAGAGCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTT
genomic: GGAAGAAGTTTTGGAACTTGTTCCACCTACAGCCAATGCGAGACCAGAAAgtactcactg ... gggtatgtagGGAGAGCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTT

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: 48 (upstream exon), 27 (downstream exon)
Score: 28

GGAAGAAGTTTTGGAACTTGTTCCACCTACAGCCAATGCGAGACCAGAAAgtactcactg ... gggtatgtagGGAGAGCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTTGAACCCCTTAGGAATCGTCTCTCTGAGAACACTGAACTACAAAGTGCTA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 205

GGAAGAAGTTTTGGAACTTGTTCCACCTACAGCCAATGCGAGACCAGAAAgtactcactg ... gggtatgtagGGAGAGCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTTGAACCCCTTAGGAATCGTCTCTCTGAGAACACTGAACTACAAAGTGCTA


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 41

GGAAGAAGTTTTGGAACTTGTTCCACCTACAGCCAATGCGAGACCAGAAAgtactcactg ... gggtatgtagGGAGAGCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTTGAACCCCTTAGGAATCGTCTCTCTGAGAACACTGAACTACAAAGTGCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

GGAAGAAGTTTTGGAACTTGTTCCACCTACAGCCAATGCGAGACCAGAAAgtactcactg ... gggtatgtagGGAGAGCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTTGAACCCCTTAGGAATCGTCTCTCTGAGAACACTGAACTACAAAGTGCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcacacttgttcatgtggtaccgtgcacactcattttattatttgggtatgtagGGAGAGCTTCAATACTTCATTGGAGTTCAATTGGATGGAAGCGACCATGTTGAACCCCTTAGGAATCGTCTCTCTGAGAACACTGAACTACAAAGTGCTA
                             actcattttattattt  TA-rich tract