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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatttttcttattgctgcctgtttcccagtttccagtttctgccaacaacagttcttgacaatcacaataaaaatggctcttgtgcttattttctgcctttccaaacactgatttattaacgacggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG

Basic information

species Zea mays
transcript GRMZM2G104632_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 8
gtcatttttcttattgctgcctgtttcccagtttccagtttctgccaacaacagttcttgacaatcacaataaa--aatggctcttgtgcttatt-----ttctgcctttccaa--acactgatttattaacgacgg-tgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG
                        ||  |  |||| | |  |||  |  |      | |   ||||| || |||  | | ||||||||| || ||     ||  | |  |||||     || ||| ||   | | || | |||||||||||||||||||||||||||| || ||||| || ||||||||||||||||| |||||||
-------------------gtaacttatctatttctaatc-ctgttactattttcccattttaatcataacaaacaatttgctcttgtgatttttcatattttcgtccatccaatggagctaattgatattccatgggtatgcagGTTGTCCATGAGGAATTTGGCATTGTTGAGGGTCTCATGACAACTGTTCATGCCACAACAG

upper sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 3'ss of exon 8
gtcatttttcttattgctgcctgtttcccagtttccagtttctgccaacaacagttcttgacaatcacaataaaaatggctcttgtgcttattttctgcctttccaaacactgatttattaacgacggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG
                |     ||  || |  |      ||||||||||     ||  ||| || |   |    |     ||||       |||||  | | ||| ||  ||| ||        | | | | |||||||| |||||||||||||| ||||| |||||  | ||||||||||| ||||| || ||||
---------------accaaacgtaacctacatgttttcttctgccaac-----ttaatgaaaaccctcacttcatcatttctt-------ttttcaacttgtcctaaacctggtt--------atgctttacagGTTGTTCATGAGGAATTTGGTATCGTTGAGGGTTTAATGACAACTGTGCATGCCACTACAG
















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|29576993|gb|CB617105.1|CB617105
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|31354565|gb|CD438922.1|CD438922
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|60397796|gb|DN230612.1|DN230612
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|211318619|gb|FL124696.1|FL124696
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|31352951|gb|CD437308.1|CD437308
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|211011830|gb|FL066256.1|FL066256
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|67017162|gb|CO445911.1|CO445911
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|211009063|gb|FL066254.1|FL066254
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|21088933|gb|BQ401246.1|BQ401246
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|6564069|gb|AW231691.1|AW231691
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|28987666|gb|CB351748.1|CB351748
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GGTGTCCATGAGGAATTTGGCATCGTGGAGG
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGG
EST: gi|24769367|gb|CA404496.1|CA404496
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|32945687|gb|CF050506.1|CF050506
EST:     TTGTTTCTAATGCAAGTTGCACTACCTTCTTCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|5928870|gb|AW056162.1|AW056162
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|32857247|gb|CD996928.1|CD996928
EST:     TGTTTCTAATGCAAGTTGCACCACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|71449917|gb|DR830967.1|DR830967
EST:     CAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: CAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|60355829|gb|DN222802.1|DN222802
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|71320203|gb|DR796854.1|DR796854
EST:     TTGTTTTTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|211011829|gb|FL066255.1|FL066255
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
EST: gi|211318615|gb|FL124692.1|FL124692
EST:     TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAG                         GTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT
genomic: TTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCAT

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: 332

CATGTTTGTAGTTGGAGTTAATGAGAATAGCTATGATCCAAAGATGAATGTTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 230

CATGTTTGTAGTTGGAGTTAATGAGAATAGCTATGATCCAAAGATGAATGTTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

CATGTTTGTAGTTGGAGTTAATGAGAATAGCTATGATCCAAAGATGAATGTTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 440

CATGTTTGTAGTTGGAGTTAATGAGAATAGCTATGATCCAAAGATGAATGTTGTTTCTAATGCAAGTTGCACTACCAACTGCCTTGCTCCACTTGCCAAGgtcatttttc ... cggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgtgcttattttctgcctttccaaacactgatttattaacgacggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG
                                    tattaac  putative branch site (score: 440)
                               tgatttattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatttttcttattgctgcctgtttcccagtttccagtttctgccaacaacagttcttgacaatcacaataaaaatggctcttgtgcttattttctgcctttccaaacactgatttattaacgacggtgtgcagGTTGTCCATGAGGAATTTGGCATCGTGGAGGGCCTTATGACAACTGTTCATGCAACAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG