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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtctataagttgccttagcttggttgtctataattgtcagtttttgctaaaacttgaaatcgccaagcattttcagacgatgtttccctttatcttactccattaaatcttgaagtcttgtatgctttcaaatggtttcagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA

Basic information

species Zea mays
transcript GRMZM2G128877_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 9
gtttgtctataagttgccttagct--------tggttgtctataattgtca-----gtttttgctaaaacttg------aaatcgccaagcattttcagacgatgtttccctttatcttactccattaaatc--ttgaagtcttgtatgctttcaaatggtttcagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
||||||  | ||  | || | | |        |  |  | | |  || ||       |||||  |||   ||        || | | ||    |   ||    ||||| ||      ||  || | | ||    |  || |||| ||| |||| ||| | |  ||||||||||| |||||| | |||||||||||||| ||||| || ||||| ||||| || || ||||||||||| || |||||||||||||||||||||||||
gtttgtacagaacctaccatggttctcactcataataatatgtgcttttcctccccatttttattaaggtttctgtgttgaaccactaaatgctcaaag-tactgttttccccctcttttttctactcaactaatctaattcttatatacttttaaacgatcccagCGTGTACTTGATGCATTGTTCCCCTCAGTTCTTGGAGGAACATGTGCCATTCCTGGAGCTTTTGGTTGTGGAAAGACTGTCATTAGTCAGGCACTTTCCA

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 9
gtttgtctataagttgccttagcttggttgtctataattgtcagtttttgctaaaacttgaaatcgccaagcattttcagacgatgtttccctttatcttactccattaaatcttgaagtcttgtatgctttcaaatggtttcagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
                                                           | || |  ||    ||  ||   | | |   || | |||| | |    ||   ||| | |  |   |||  |||   |  || |||||||| || ||||| || |||||||||||||| || || |||||||| ||||| || || ||||||||||||||||| |||||||||||||| ||||| |
-----------------------------------------------------------gtaaac-tcagttgttaccaagtg-tctcctccatgatctaattgtgatag-ccttcatgctta--atgacttctgttttttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATTCCTGGTGCTTTTGGTTGTGGTAAAACAGTCATTAGTCAGGCTCTTTCTA

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 9
gtttgtctataagttgccttagcttggttgtctataattgtcagtttttgctaaaacttgaaatcgccaagcattttcagacgatgtttccctttatcttactccattaaatcttgaagtcttgtatgctttcaaatggtttcagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
                                                           | || |  ||    || |||   | | |   || | |||| | |    ||  | |     |     |||  |||   |  || |||||||| || ||||| || |||||||||||||| || || |||||||| || || || || |||||||||||||||||||||||||||||||| ||||| |
-----------------------------------------------------------gtaaac-tcagttgttatcaagtg-tctcatccataatctaattgtgatagctttc---atgcgtaatgacttctgctttttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATACCTGGAGCTTTTGGTTGTGGTAAAACTGTCATTAGTCAGGCTCTTTCTA

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
gtttgtctataagttgccttagcttggttgtctataattgtcagtttttgctaaaacttgaaatcgccaagcatt-ttcagacgatgtttccctttatcttactccattaaatcttgaagtcttgtatgctttcaaatggtttcagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
                                                          |||   | | |   ||| |||  ||  || |     | || | | | |||    |  |||    |||  | ||||    || | ||||||||| || ||||| || ||||| || ||||| || || || ||||| ||||| || || ||||| ||||| |||||||| || ||||||||||||||||
---------------------------------------------------------gtgattactcgattaattcttcttacagtggtgatagtcatttgaatacatgtgttgctga----ttgctttcttttcc-tgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 9
gtttgtctataagttgccttagcttggttgtctataattgtcagtttttgctaaaacttgaaatcgccaagcattttcagacgatgtttccctttatcttactccattaaatcttgaa-gtcttgtatgctttcaaatggtttcagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
                                               |   ||  |    || |    | | ||| ||||    | ||  | | |||    || |  |||   |  |  || ||      |||    |  | ||||||||| || ||||| || ||||| || ||||| || || |||||||| || || ||||||||||||||||| ||||| ||||| ||||| || ||||| |
----------------------------------------------gtaattagcatacaaactaa--atgtattatcag----tattctcatctatg--gctgctgtaagcttgaagtgtgttcctgatttttgtttcatctcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTA

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 9
gtttgtctataagttgccttagcttggttgtctataattgtcagtttttgctaaaacttgaaatcgccaagcattttcagacgatgtttccctttatcttact-ccatt---aaatcttgaagtcttgtatgctttcaaatggttt-cagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
                                                                 |  | ||||  |   | | | ||  ||  ||  | ||| |||||   ||||    |  |||  ||   | |    |  | | |||||||| || ||||| || || |||||||| ||||| || |||||||| ||||| ||||||||||| ||||| ||||| ||||| ||||| || |||||||
-----------------------------------------------------------------gtaatgcatcctgtcaaggt-ttagcccatacatgactaccattttgaaatgggtatttctgatactttcttttgtactctacagCGTGTTCTCGATGCTCTCTTTCCCTCAGTCCTGGGTGGGACTTGTGCAATTCCTGGGGCATTTGGCTGTGGGAAAACAGTCATCAGTCAAGCTCTTTCCA

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 6
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 9
gtttgtctataagttgccttagcttggttgtctataattgtcagtttttgctaaaacttgaaatcgccaagcattttcagacgatgtttccctttatcttac---tccattaaatcttgaagtcttgtatgctttcaaatggttt-cagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
                                           ||||      ||| |    |  |  ||| || || | | | |  || | | | |  |     |   | || | ||      ||||    | |       ||| |||||| |||||||||| |||||||| || ||||| ||||| ||||| || ||||| || |||||||| ||||| || |||||||||||||| || || || |
------------------------------------------ggtttc-----aaattcatgactg--aagtatatttatatgttacttacatgtgtgctgtgaatatctcaagtattttctctttgttgattgttgtcccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA

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|116813623|gb|EC856086.1|EC856086
EST:     GGCCTGTTGCGTCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAG                         CGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATT
genomic: GGCCTGTTGCGTCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggtttcagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATT
EST: gi|13516146|gb|BG518422.1|BG518422
EST:     TCTGACAGGGCAG                         CGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATT
genomic: TCTGACAGGGCAGgtttgtctat ... atggtttcagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATT

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: 287

ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCGTCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggtttcagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 460

ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCGTCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggtttcagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 329

ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCGTCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggtttcagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 480

ACATGGCCTGTGCGTTCACCAAGGCCTGTTGCGTCGAAGCTTGCTGCGGATACACCTCTTCTGACAGGGCAGgtttgtctat ... atggtttcagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttatcttactccattaaatcttgaagtcttgtatgctttcaaatggtttcagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA
     atcttac  putative branch site (score: 480)
               attaaatctt  TA-rich tract