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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaggttcgttgtggtgcatggtagcttaacctggtgaaagatgttacagctatactaatgtagaatatgaaaagcttattctttcctgttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATGTTTTATCTTGCTGCTGCAGTTTCCGACTTCTATGTTCCATGGGAAAGTA

Basic information

species Zea mays
transcript GRMZM2G008209_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008209_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g07880.1 (Oryza sativa), 3'ss of exon 7
---aaaaggttcgttgtggtgcatggta---gcttaacctggtgaaagatgttacagctatactaatgtagaatatgaaaagcttattct-ttcctgttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATGTTTTATCTTGCTGCTGCAGTTTCCGACTTCTATGTTCCATGGGAAAGTA
    ||   |  ||| || |  |  |||   | ||||||| |  |       ||| | |||||| |||  |||| ||| |    | ||||  |  | || |  | ||||||| |||||||| | |||  | |||||||||||||| | ||  ||||||||||| |||||||| |||||||| ||||| ||||||||||||||||| |
tgccaattttctgttatgttctacagtaaaagattaaccttggca-------tactgttatactgatgaggaatctgatatatctcttctgcttgtttttccaatagTTACTGCAAATGGTAGGTACGGCGATGAATTGCTTGGGACGCCAAGGAATGTTTTACCTTGCTGCGGCAGTTTCTGACTTTTATGTTCCATGGGAAAGCA

upper sequence: GRMZM2G008209_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G12350.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------------aaaaggttcgttgtggtgcatg----gtagcttaacctggtgaaaga--tgttacagct-atactaatg----tagaatat-------------gaaa---agcttattctttcctgt--tgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATGTTTTATCTTGCTGCTGCAGTTTCCGACTTCTATGTTCCATGGGAAAGTA
                                 |  | || ||  ||   |||     |||   | | |||   ||  |    ||| |  | ||   ||||    | | || |             | ||   || ||||| ||   ||   | |  |||| |  | |   || | |||||     ||||     | || |   ||   |||||||||||||||||||| || || ||||||||||| ||||||  ||| |
gttcttaaatcttacactagctacttcagtcatattgttttgtcttgacacataaaatgtaatcttaactgcctaagaaaccattagaatttatctcaatgcttgtgggatttctttaacagggctgcaactgagattatttttctttggaatacaaacagATGTTGCGGTTGATTGCTACGATATTGAAAGATGTCGGTCCATGTTCGATGTTTTATCTTGCTGCTGCTGTATCTGACTTCTATGTGCCATGGTTAAGCA

upper sequence: GRMZM2G008209_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT5G02080.1 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------aaaaggttcgttgtggtgcatggtagctt------aacctggtgaaagatgttacagctatactaatgtagaatatgaaaagctta---ttctttcctgttgctgacagTT---ACTACAAATG--GTGGCTACTTCTA-------TGAATTGCTTGGGGCACCGTGGAATGTTTTATCTTGCTGCTGCAGTTTCCGACTTCTATGTTCCATGGGAAAGTA
                                    |   ||| ||   || ||| ||       || |||    ||   ||       || ||     |||      |  ||| |   | ||||| | |||   |   ||     |||| |||  | || |  ||  |       ||||     | || |   ||  ||||||||||||||||||||| || || ||||||||||| |||||| | || |
gttcttcgatcttacaccaagctaatctttgttttttgtcttgaggcatatagtaactgcaaaagaaactgccataaagcgtagtgagaattcttcaacagagctgccatggctgaaattactttctttttgtgaatgtttctggttacagATGTTGCGGTTGATTGCAGAGGCATTGAAAGATGTTGGTCCATGTTCAATGTTTTATCTTGCTGCTGCTGTATCTGACTTCTATGTGCCATGGAAGAGCA

upper sequence: GRMZM2G008209_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g04420.t01 (Vitis vinifera), 3'ss of exon 7
aaaaggtt--cgttgtggtgcatggtagcttaacctggtgaaagatgttacagctatac-taatgtagaatatgaaaagcttattctttcctgttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATGTTTTATCTTGCTGCTGCAGTTTCCGACTTCTATGTTCCATGGGAAAGTA
 |    ||  | || |  | |||  | |   |   |  ||| |          |   |  || |   |   || |||   ||  ||||| |  | |    ||| |  |||| | | | ||     | ||||      | ||    |  ||||||||||| ||||| |||||||| || ||||| |||||||||||| | || |
-atttcttgccattttcattcatatttgtcaacagttatgagaagctccttttcagcaagtagttctgtccattaaatatttgatctttgcattgg--agcagATTTTACACAAGATTGCAGTACCAATGAGGACTCTAGGAGGACAAGGAATGTTTTACCTTGCAGCTGCAGTATCAGACTTTTATGTTCCATGGAACAGCA

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|78110994|gb|DV529391.1|DV529391
EST:     AATGCCTTCTTCTCAAACTGCCTTTCACAACAATTTTTGAGTACCTTCAG                         TTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATG
genomic: AATGCCTTCTTCTCAAACTGCCTTTCACAACAATTTTTGAGTACCTTCAGgtattgcacc ... ttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATG
EST: gi|71318838|gb|DR796180.1|DR796180
EST:     TTTTTGAGTACCTTCAG                         TTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATG
genomic: TTTTTGAGTACCTTCAGgtattgcacc ... ttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATG
EST: gi|86469977|gb|DY236347.1|DY236347
EST:     AATGCCTTCTTCTCAAACTGCCTTTCACAACAATTTTTGAGTACCTTCAG                         TTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATG
genomic: AATGCCTTCTTCTCAAACTGCCTTTCACAACAATTTTTGAGTACCTTCAGgtattgcacc ... ttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATG
EST: gi|74246159|gb|DT654073.1|DT654073
EST:     AATGCCTTCTTCTCAAACTGCCTTTCACAACAATTTTTGAGTACCTTCAG                         TTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATG
genomic: AATGCCTTCTTCTCAAACTGCCTTTCACAACAATTTTTGAGTACCTTCAGgtattgcacc ... ttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATG
EST: gi|71307842|gb|DR790142.1|DR790142
EST:     AATGCCTTCTTCTCAAACTGCCTTTCACAACAATTTTTGAGTACCTTCAG                         TTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATG
genomic: AATGCCTTCTTCTCAAACTGCCTTTCACAACAATTTTTGAGTACCTTCAGgtattgcacc ... ttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATG
EST: gi|71756861|gb|DR954798.1|DR954798
EST:     AATGCCTTCTTTTCAAACTGCCTTTCACAACAATTTTGGAGTACCTTCAG                         TTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATG
genomic: AATGCCTTCTTCTCAAACTGCCTTTCACAACAATTTTTGAGTACCTTCAGgtattgcacc ... ttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATG
EST: gi|78120327|gb|DV538711.1|DV538711
EST:     CAAACTGCCTTTCACAACAATTTTTGAGTACCTTCAG                         TTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATG
genomic: CAAACTGCCTTTCACAACAATTTTTGAGTACCTTCAGgtattgcacc ... ttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATG

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: 39 (upstream exon), 47 (downstream exon)
Score: 12

GCAATCGATGAATGCCTTCTTCTCAAACTGCCTTTCACAACAATTTTTGAGTACCTTCAGgtattgcacc ... ttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATGTTTTATCTTGCTGCTGCAGTTTCCGACTTCTATGTTCCATGGGAAAGTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 26

GCAATCGATGAATGCCTTCTTCTCAAACTGCCTTTCACAACAATTTTTGAGTACCTTCAGgtattgcacc ... ttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATGTTTTATCTTGCTGCTGCAGTTTCCGACTTCTATGTTCCATGGGAAAGTA


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

GCAATCGATGAATGCCTTCTTCTCAAACTGCCTTTCACAACAATTTTTGAGTACCTTCAGgtattgcacc ... ttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATGTTTTATCTTGCTGCTGCAGTTTCCGACTTCTATGTTCCATGGGAAAGTA


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 24

GCAATCGATGAATGCCTTCTTCTCAAACTGCCTTTCACAACAATTTTTGAGTACCTTCAGgtattgcacc ... ttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATGTTTTATCTTGCTGCTGCAGTTTCCGACTTCTATGTTCCATGGGAAAGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacagctatactaatgtagaatatgaaaagcttattctttcctgttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATGTTTTATCTTGCTGCTGCAGTTTCCGACTTCTATGTTCCATGGGAAAGTA
         tactaat  putative branch site (score: 24)
                               cttattctttcctgtt  putative PPT
                    aatatgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaggttcgttgtggtgcatggtagcttaacctggtgaaagatgttacagctatactaatgtagaatatgaaaagcttattctttcctgttgctgacagTTACTACAAATGGTGGCTACTTCTATGAATTGCTTGGGGCACCGTGGAATGTTTTATCTTGCTGCTGCAGTTTCCGACTTCTATGTTCCATGGGAAAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG