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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgatatacccttgaatcgtacagcttatggagttgtatttgctttgtgtttctgtttttttataattctttgctttaaattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA

Basic information

species Zea mays
transcript GRMZM2G157462_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 17
gttgatatacccttgaatcgtacagcttatggagttgtatttgctttgtgtttctgtttttttataattctttgctttaaattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA
||| | ||  || |||||    ||||||   || ||   ||| |||| |    |  || || | ||| |  | |  ||   |||| ||||||| ||||||||||| || || |||||||||| ||||||||| ||||||||||||||||||||    ||||| ||||| ||||||||||| || |||||
gttaagat--ccctgaatacctcagctt---gattt---ttttctttataagacccttgttgtctaaatggt-gtatttccttttacagCTCATAGTGCTGTTGTATTGAAAGCTGAGAGCACGGCCGACAAAGTTGAGTGGGTAAATAAGATACGGGCTGTAATTCAAAGCAAAGGGGGATCATTCAA

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 17
---------------------gttgatatacccttgaatcgtacagcttatggagttg--tatttgctttgtg---tttctgtttttttataattctttgctttaaattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA
                       || |    ||   |   || |   ||    | |     |   | | ||     |  ||    | | | |||  |      || ||||||||||||| ||||| ||| |||||||||||||||| ||||| || |||||||||||| | || ||| | | |  ||||   |||   ||||| |||     || 
gtaatccctcttgttctaatttatggttcctcccccacctgttccaattccaaaatgcatcaccagatctgaacaatgcctcgactgtgacaatattaaatcatacattttgcagCTCAAAGTGCAGTTTTGTTAAAGGCTGAGAGTATGGCAGATAAGGTTGAGTGGATCAACAAGTTAAGAAGTGTTGCACAGGCTAAAGGAGGTCAAGCCAT

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 17
---------------------gttgatatacccttgaatcgt-acagcttatggagttgt-atttgctttgtg---tttctgtttttttataattctttgctttaaattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA
                       ||||    ||   |   || |||  |     |    | |   | | ||     |  ||    | | | |||  |    | || ||||||||||| | ||||| ||| |||||||||||||||| ||||| || |||||||||||| | || ||| | | |  ||||   |||   ||||| |||     || 
gtaatccctattgttctaatttatgattcctcccccacctgttacaattccaaaatccatcaccagatctgaacaatgccttgactgtgacaatattgaattatacattttgcagCTGAAAGTGCAGTTTTGTTAAAGGCTGAGAGTATGGCAGATAAGGTTGAGTGGATCAACAAGTTAAGAAGTGTTGCACAGGCTAAAGGAGGTCAAGCCAT

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 17
-gttgatatacccttgaatcgtacagct-tatggagttgtatttgctttgtgtttctgtttt--tttataattct-------------ttgctttaaattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAG---CAAAGGGGGTTCTTTCAA
  ||| | |   | |   || |   ||| ||   || || ||   | |   |||| ||||||   ||| |||| |             ||    | ||| ||||||| ||||||||||| ||| | ||||| ||||| ||||| || || ||||| |||||||| ||||| |    |||||||||      ||||||||||    |   
gtttgttcttgtcctagttcattgtgctctacttaggtggatagtcctctggtttttgttttgacttacaattttaaataaaacaaatttttaattaatcttgcagCCCACAGTGCTGTGGTGCTTAAGGCAGAGAGTATGGCAGATAAAGTTGAATGGGTAAACAAGATAAGCAGTGTTATTCAACCTTCCAAAGGGGGTCAAAT---

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 17
---------------gttgat-atacccttgaatcgtacagcttatggagttgtatttgctttgtgtttc-tgtttttttataatt--ctttgc-tttaaatttt-----------gcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA
                |||||  |||  |||    || | |||| |||| |  | |    ||    | || | |||  ||| || |   ||| |  |||||||||           ||||||||||||||||||||||||||||||||||||   |  || |||| ||||||| |||| ||  | | |  ||||||||||     |||            
gtacgtttttcatcttttgattgtacttttg----gtcctgcttgtggactgttgtcattttcccctctcctatttaattacaagtgattttacacttaaattttccatttatcatgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCGCAGTGGATAAGGCTGAGTGGTTAAACAAATTGAGAAATGTTATTCAGCCTTCAGGTCAAGTGAAGGG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv02s0087g00010.t01 (Vitis vinifera), 3'ss of exon 2
----gttgatatacccttgaatc--------gtacagcttatgga--gttgt-atttgc---tttgtgtttctgtttttttataattc--tttgctttaaattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA
    |||  ||| |  |||| |         || | |||| ||||  ||||| |||| |   | |    ||  ||  ||||| | ||   ||| |  |  ||  |||||||||||||||||||||||||||||||||||||   || || |||| ||||||| |||| ||  | | |  ||||||||||     |||            
gtacgttattattcttttgactgtacttctagtcctgcttgtggactgttgtcattttcccctctcctatttagtgattttacacttaaattttccatttatcatgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCGCAGCGGATAAGGCTGAGTGGTTAAACAAATTGAGAAATGTTATTCAGCCTTCAGGTCAAGTGAAGGG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv03s0110g00120.t01 (Vitis vinifera), 3'ss of exon 2
----gttgatatacccttgaatc--------gtacagcttatggagttgtatttgctttgtgtttc-tgtttttttataatt--ctttgc-tttaaatttt-----------gcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA
    |||  ||| |  |||| |         || | |||| || | |  | |    ||    | || | |||  ||| || |   ||| |  |||||||||           ||||||||||||||||||||||||||||||||||||   || || |||| ||||||| |||| ||  | | |  ||||||||||     |||            
gtacgttattattcttttgactgtacttctagtcctgcttgtgtactgttgtcattttcccctctcctatttaattacaagtgattttacacttaaattttccatttatcatgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCGCAGCGGATAAGGCTGAGTGGTTAAACAAATTGAGAAATGTTATTCAGCCTTCAGGTCAAGTGAAGGG

upper sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv03s0038g00540.t01 (Vitis vinifera), 3'ss of exon 2
----gttgatatacccttgaatc--------gtacagcttatggagttgtatttgctttgtgtttc-tgtttttttataatt--ctttgc-tttaaatttt-----------gcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA
    |||  ||| |  |||| |         || | |||| |||| |  | |    ||    | || | |||  ||| || |   ||| |  |||||||||           |||| ||||||||||||| ||||||||||||||||||| || || |||| ||||||| |||| ||  | | |  ||||||||||     |||            
gtacgttattattcttttgactgtacttctagtcctgcttgtggactgttgtcattttcccctctcctatttaattacaagtgattttacacttaaattttccatttatcatgcagTTCACAGTGCTGTTATGTTAAAGGCTGAGAGCATAGCGGATAAGGCTGAGTGGTTAAACAAATTGAGAAATGTTATTCAGCCTTCAGGTCAAGTGAAGGG

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|12046697|gb|BF728836.1|BF728836
EST:     TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAG                         CTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
genomic: TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAGgttgatatac ... aattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
EST: gi|78180891|gb|DV551264.1|DV551264
EST:     TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAG                         CTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
genomic: TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAGgttgatatac ... aattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
EST: gi|31353959|gb|CD438316.1|CD438316
EST:     TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAG                         CTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
genomic: TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAGgttgatatac ... aattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
EST: gi|22491320|gb|BU051243.1|BU051243
EST:     TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAG                         CTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
genomic: TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAGgttgatatac ... aattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
EST: gi|32847552|gb|CD987233.1|CD987233
EST:     TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAG                         CTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
genomic: TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAGgttgatatac ... aattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
EST: gi|87151847|gb|DY396636.1|DY396636
EST:     TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAG                         CTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
genomic: TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAGgttgatatac ... aattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
EST: gi|19437242|gb|BM953652.1|BM953652
EST:     TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAATG                         CTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
genomic: TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAGgttgatatac ... aattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
EST: gi|32857965|gb|CD997646.1|CD997646
EST:     GCTTGGATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAG                         CTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
genomic: TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAGgttgatatac ... aattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
EST: gi|31354322|gb|CD438679.1|CD438679
EST:     TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAG                         CTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
genomic: TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAGgttgatatac ... aattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
EST: gi|7031283|gb|AW461021.1|AW461021
EST:     TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAG                         CTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT
genomic: TCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAGgttgatatac ... aattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGT

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), 49 (downstream exon)
Score: 175

AAAAGTTCAAAGGACTCAAAAAAGGCAAATGGATCAGAAAAAATCTCAAGTCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAGgttgatatac ... aattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

AAAAGTTCAAAGGACTCAAAAAAGGCAAATGGATCAGAAAAAATCTCAAGTCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAGgttgatatac ... aattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 237

AAAAGTTCAAAGGACTCAAAAAAGGCAAATGGATCAGAAAAAATCTCAAGTCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAGgttgatatac ... aattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

AAAAGTTCAAAGGACTCAAAAAAGGCAAATGGATCAGAAAAAATCTCAAGTCTTGTATTTAAGATTACTAATAGGGTTGCATACAAAACGGTCCTCAAAGgttgatatac ... aattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtatttgctttgtgtttctgtttttttataattctttgctttaaattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA
                tttctgtttttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgatatacccttgaatcgtacagcttatggagttgtatttgctttgtgtttctgtttttttataattctttgctttaaattttgcagCTCACAGTGCTGTTGTGTTAAAGGCTGAGAGCATGGCCGACAAGGTTGAGTGGGTAAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG