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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcacatcatctgttcataccagaaataagaaaaaaaactgcatttggcttattctgtttgtaacgtggtaatctttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTT

Basic information

species Zea mays
transcript GRMZM2G060896_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060896_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 4
--------gttcacatcatctgttcataccagaaataagaaaaaaaact-gcatttggcttattctgt-ttgtaacgtggtaa---------tctttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTT
         ||| ||||| || || | | |  |||||| ||||||| || | ||||    || | ||| ||  |  || ||           | ||| ||||||||| || |||||||| ||||| ||||| |||||||||||||| ||||||||||| |||||||||||||| ||||||||||||||||||||||| || ||||
gttctcaacttctcatcacctattgacagccaaaataaaaaaaaaatctagtatttattatactttgtattacagtgttgtgtgacctgttttttttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTTCCGCTTT

upper sequence: GRMZM2G060896_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G13210.3 (Glycine max), 3'ss of exon 4
gttcacatcatctgttcataccagaaataagaaaaaaaactgcatttggcttattctgtttgtaacgtggtaatctttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTT
       |  ||| |||||   |  | | |  | |||   | |||     | ||         |   |  |  | ||  | ||||||| || |  ||||| || || ||||| |||||||| || ||||| |||||||| | |||||||||||| |||||||| |||||  |||| || || || |
----gtttggtctcttcatcttatgatttactataaattttacatgaaagtgat-------aaatgctaatccttttgttttgcagTCATCAATGTATGGGAATGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAGGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT

upper sequence: GRMZM2G060896_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 4
gttcacatcatctgttcataccagaaataagaaaaaaaactgcatttggcttattctgtttgtaacgtggtaatctttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTT
       |   || |||||   | |   | | |  | ||||    ||  | |     |  |  |   |  |  | |   | ||||||| || || ||||| ||||| ||||| |||||||| || ||||| |||||||| |||||||||||||| |||||||| |||||  |||| || || || |
----gtttggcctcttcatcttata---atgtactataact----ttaacgtgaaagggatagatgctaatcctttcattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAAGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT

upper sequence: GRMZM2G060896_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------gttcacatcatctgttcataccagaaataagaaaaaaaactgcatttggcttattctgtttg-----taacgtggtaatctttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTT
                                       ||| || |  | |     |   |   ||  |  |      |   ||     |  | | || |     ||| |  |     ||| | ||||||||||  | ||||| ||||| |||||||||||||| |||||||||||||  || || ||||||||||| || ||||| |||||| ||||||| || ||||
gttctgcattctgaactctaaatactagtgttgttcgaagttgacttagtttccattttttatctatctgtcatgttcttcttttctttcttctatattagctagctaatgcagattcttttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT

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|211229918|gb|FL287074.1|FL287074
EST:     AGATCTTGTACCAGGGGAAATCGCCATACCAAGAAGTCTTAGTCTTCGAG                         TCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
genomic: AGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAGgttcacatca ... ttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
EST: gi|211227859|gb|FL287069.1|FL287069
EST:     AGATCTTGTACCAGGGGAAATCGCCATACCAAGAAGTCTTAGTCTTCGAG                         TCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
genomic: AGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAGgttcacatca ... ttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
EST: gi|148991840|gb|EE033431.2|EE033431
EST:     AGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAG                         TCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
genomic: AGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAGgttcacatca ... ttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
EST: gi|211227858|gb|FL287068.1|FL287068
EST:     AGATCTTGTACCAGGGGAAATCGCCATACCAAGAAGTCTTAGTCTTCGAG                         TCGTCGACCTATGGTAAAGTCCTT
genomic: AGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAGgttcacatca ... ttgtatgcagTCGTCGACCTATGGTAAAGTCCTT
EST: gi|211229916|gb|FL287072.1|FL287072
EST:     AGATCTTGTACCAGGGGAAATCGCCATACCAAGAAGTCTTAGTCTTCGAG                         TCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
genomic: AGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAGgttcacatca ... ttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
EST: gi|71305271|gb|DR788769.1|DR788769
EST:     AGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAG                         TCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
genomic: AGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAGgttcacatca ... ttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
EST: gi|6918561|gb|AW400091.1|AW400091
EST:     AGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAG                         TCGTCGACCTATGGTAAAGTCCTTGGGCTTGATGGTATTGGTCAGTTGACT
genomic: AGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAGgttcacatca ... ttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
EST: gi|211227857|gb|FL287067.1|FL287067
EST:     AGATCTTGTACCAGGGGAAATCGCCATACCAAGAAGTCTTAGTCTTCGAG                         TCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
genomic: AGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAGgttcacatca ... ttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
EST: gi|148946476|gb|EC891786.2|EC891786
EST:     AGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAG                         TCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
genomic: AGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAGgttcacatca ... ttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
EST: gi|74240569|gb|DT648483.1|DT648483
EST:     AGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAG                         TCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT
genomic: AGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAGgttcacatca ... ttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACT

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), 49 (downstream exon)
Score: 67

GAGAGGCCAATTCTTTGAAAGTGGAGAAGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAGgttcacatca ... ttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

GAGAGGCCAATTCTTTGAAAGTGGAGAAGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAGgttcacatca ... ttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 148

GAGAGGCCAATTCTTTGAAAGTGGAGAAGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAGgttcacatca ... ttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTT


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

GAGAGGCCAATTCTTTGAAAGTGGAGAAGATCTTATACCAGGGGAAATCGCTATACCAAGAAGTCTTAGTCTTCGAGgttcacatca ... ttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaaactgcatttggcttattctgtttgtaacgtggtaatctttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTT
                            ttgtaac  putative branch site (score: 44)
                                          tctttgt  putative PPT
                                       taatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcacatcatctgttcataccagaaataagaaaaaaaactgcatttggcttattctgtttgtaacgtggtaatctttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG