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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcggcttcaagtttcattttgttccttttgctaagataatgcgtattgtttcagtgtgagagctgtactgtactgaactggtcagtgcttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTTGATCCTCAGGCTTACAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT

Basic information

species Zea mays
transcript AC208327.4_FGT003
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC208327.4_FGT003 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g03990.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------------------------------------tttcggcttcaagtttcattttgttcctt---ttgctaagataatgcgtattgtttcagtgtgagagctgtact----gtactgaactggtcagtgcttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTTGATCCTCAGGCTTACAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT
                                                                                        |  | ||    | || ||||| ||  |   || ||||| ||| ||  |||| | | ||    |  ||           ||||| ||| | |||  ||| | | |||| |||||||| || || |||||||||||||| ||||||||||| ||||| ||||||||||||||||||||||||||||| |||  |||||||||| | |
gtgagagggcatttacatgccaattattacaagcaaatgcacacatagtttttttagtcgcagtgagagggaaaggttcgatgtgtgattagttttttttctccttttggtctataatttcctaagctaaggcaaattgctcctgtcactgcccttcgaaagaaacactgacctgattagtatttcttgtcagGTATGGCAACCTGGCGTGGATACACTGGAAGAGGGGGAGGAGCTCCAGTTCGATCCTCAGGCTTACAATTATCTCCGAGGGTTTAACATTGGCTGGCCAT

upper sequence: AC208327.4_FGT003 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g03822.1 (Oryza sativa), 3'ss of exon 2
tttcggcttcaagtttcattttg-ttccttttgctaagataatgcgtattgtttcagtgtgagagctgtactgtactgaactggtcagtgcttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTTGATCCTCAGGCTTACAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT
|||    |||   | |  ||||  || | |  ||||||  ||   |  |  | ||| ||         |     ||||| | | |  ||  ||| ||| |||| |||||||| ||||| |||||||||||||| ||||||||||| ||||| |||||||||||||||||||||||| |||| |||  |||||||||| | |
tttttttttctcctatagttttaatttcctaagctaaggcaaattgc-tcctgtcactgctcttcgaatgaaacactgacccgattggtatttcttttcagGTATGGCAACCTGGTGTGGATACACTGGAAGAAGGGGAGGAGCTCCAGTTCGATCCTCAGGCTTACAATTATCTCAGAGGGTTTAACATTGGCTGGCCGT
















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|20811103|gb|BQ295581.1|BQ295581
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|78089597|gb|DV517971.1|DV517971
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|211516191|gb|FL166755.1|FL166755
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|26456410|gb|CA827993.1|CA827993
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|33467487|gb|CF244536.1|CF244536
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|148933097|gb|EC876730.2|EC876730
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|211466442|gb|FL172133.1|FL172133
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|19822069|gb|BQ048093.1|BQ048093
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|211516190|gb|FL166754.1|FL166754
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
EST: gi|26457087|gb|CA828670.1|CA828670
EST:     CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAG                         GTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT
genomic: CTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTT

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: 473

AAAACTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTTGATCCTCAGGCTTACAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

AAAACTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTTGATCCTCAGGCTTACAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 198

AAAACTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTTGATCCTCAGGCTTACAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

AAAACTGAATCGTCCTCGTCGTCCAACCCTGCGATTGCCTCTGGTCCGGCTAAGgtgagggaga ... ttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTTGATCCTCAGGCTTACAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgtttcagtgtgagagctgtactgtactgaactggtcagtgcttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTTGATCCTCAGGCTTACAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT
                                            cttcgtttt  CT-rich tract
                                                 tttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcggcttcaagtttcattttgttccttttgctaagataatgcgtattgtttcagtgtgagagctgtactgtactgaactggtcagtgcttcgttttagGTCTGGCAACCGGGTGTAGATACACTGGAAGATGGGGAGGAGCTGCAGTTTGATCCTCAGGCTTACAATTATCTCCGAGGTTTTGGCATTGGCTGGTCTT

- -cggcttc
- - - - - - -tttcatt
- - - - - - - - - - - - - -ttttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtactg