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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgagggctgtcgagtttttttttccaagtgtaaataacattatagtgttacatatagattaacagtgatgcatttctgcttttctaattgcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATGGATAAGGAGATTGAAGATGTTAATGCTGATATTAAAGCTTATGAGGCTT

Basic information

species Zea mays
transcript GRMZM2G092112_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g48920.1 (Oryza sativa), 3'ss of exon 2
---ccgagggctgtcgagtttttttttccaagtgtaaat-aacattatagtgttacat---atagattaacagtgatgcatttctgcttttctaattgcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATGGATAAGGAGATTGAAGATGTTAATGCTGATATTAAAGCTTATGAGGCTT
     |  |  ||| |    |   |||    | || | |  |      | ||||| ||   |||   | | | ||||| |  |||||       | ||    |||||||||| |||||| | |||||||| ||||||||| | || ||||||||||||||||||||||||||||||||||||||||| |||||||||||||| |  |
tgtgtgttgtatgtgggaagtacatttatttgcgtgacttgatggctcattgttaaatgttatatgctgataatgatgtaaatctgc-------aatgtacttgcagGTTGAGCAGCCAATGTGTCTGGACTGTATGAGGTTGCTCTCTGATAAGATGGATAAGGAGATTGAAGATGTTAATGCTGACATTAAAGCTTATGAAGTCT

upper sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g44200.1 (Oryza sativa), 3'ss of exon 3
ccgagggctgtcgagtttttttttccaagtgtaaataacattatagtgttacatatagattaacagtgatgc-atttctgcttttcta-attgcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATGGATAAGGAGATTGAAGATGTTAATGCTGATATTAAAGCTTATGAGGCTT
  |   | | | |    | | | |  | |  | | |  |||  |  |  ||  |  |||  |||| ||     |   ||| |  |||  | |     || || ||||||||||||| |||||||| ||||||||| | || |||||||| ||||| ||||| ||||||||||||||| |||| | ||||||||||||||| |
-tgcatgtttttgctactatatgttgagggttcattgccatc-tgttagtattttgagaggaacaatgtcaagaccgctgataatctggaatatacttgtagATTGAACAGCCACTCTGTCTGGACTGTATGAGGTTGCTGTCTGATAAAATGGAGAAGGAAATTGAAGATGTTAATACTGACAATAAAGCTTATGAGGCCT
















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|31360578|gb|CD444935.1|CD444935
EST:     GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAG                         GTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATG
genomic: GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAGgtacgattga ... gcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATG
EST: gi|67020672|gb|CO449421.1|CO449421
EST:     GTGTTACTGTGCTGAAAA-GGCCTTTGAGATTGCTAGCTCGCAAACTCAG                         GTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATG
genomic: GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAGgtacgattga ... gcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATG
EST: gi|211504088|gb|FL041157.1|FL041157
EST:     GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAG                         GTTGAACAGCC
genomic: GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAGgtacgattga ... gcctgtgcagGTTGAACAGCC
EST: gi|74242757|gb|DT650671.1|DT650671
EST:     GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAG                         GTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATG
genomic: GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAGgtacgattga ... gcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATG
EST: gi|67014170|gb|CO442919.1|CO442919
EST:     GTGTTACTGTGCTGAAAA-GGCCTTTGAGATTGCTAGCTCGCAAACTCAG                         GTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATG
genomic: GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAGgtacgattga ... gcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATG
EST: gi|71764423|gb|DR962360.1|DR962360
EST:     GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAG                         GTTGAACAGCCACTTTGTCTGGGATGTATGAGGGGTCTTTCTGATAAGATG
genomic: GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAGgtacgattga ... gcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATG
EST: gi|149081324|gb|EE170439.2|EE170439
EST:     GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAG                         GTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATG
genomic: GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAGgtacgattga ... gcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATG
EST: gi|67028723|gb|CO457472.1|CO457472
EST:     GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAG                         GTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATG
genomic: GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAGgtacgattga ... gcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATG
EST: gi|29947670|gb|CB816776.1|CB816776
EST:     GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAG                         GTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATG
genomic: GTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAGgtacgattga ... gcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATG

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: 160

TGTAATCTCCAGTAGCCCCTCGCTGGGAAACAATTCTGGGTTTCACTCTAGTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAGgtacgattga ... gcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATGGATAAGGAGATTGAAGATGTTAATGCTGATATTAAAGCTTATGAGGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

TGTAATCTCCAGTAGCCCCTCGCTGGGAAACAATTCTGGGTTTCACTCTAGTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAGgtacgattga ... gcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATGGATAAGGAGATTGAAGATGTTAATGCTGATATTAAAGCTTATGAGGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

TGTAATCTCCAGTAGCCCCTCGCTGGGAAACAATTCTGGGTTTCACTCTAGTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAGgtacgattga ... gcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATGGATAAGGAGATTGAAGATGTTAATGCTGATATTAAAGCTTATGAGGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 242

TGTAATCTCCAGTAGCCCCTCGCTGGGAAACAATTCTGGGTTTCACTCTAGTGTTACTGTGCTGAAAAGGGCCTTTGAGATTGCTAGCTCGCAAACTCAGgtacgattga ... gcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATGGATAAGGAGATTGAAGATGTTAATGCTGATATTAAAGCTTATGAGGCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttacatatagattaacagtgatgcatttctgcttttctaattgcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATGGATAAGGAGATTGAAGATGTTAATGCTGATATTAAAGCTTATGAGGCTT
                                     ttctaat  putative branch site (score: 242)
       atatagattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccgagggctgtcgagtttttttttccaagtgtaaataacattatagtgttacatatagattaacagtgatgcatttctgcttttctaattgcctgtgcagGTTGAACAGCCACTTTGTCTGGAATGTATGAGGGTTCTTTCTGATAAGATGGATAAGGAGATTGAAGATGTTAATGCTGATATTAAAGCTTATGAGGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - gctgtcg
- - - - - - - - - - - - ccaagtg
- - - - - - - - - - - - - - - - -aataaca