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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggcgctgcccccttccccacttccttgctcatcgccgcgtgcggttgctcttccccgcttgatttgatgctgatttgggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACGGGGCACGGGCACCGTCAAGCTTCTCAAGAACAAGGAGACCGGCAAGGTC

Basic information

species Zea mays
transcript AC213884.3_FGT001
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC213884.3_FGT001 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g28290.1 (Oryza sativa), 3'ss of exon 1
------------gtgaggcgctgcccccttccccacttccttgctcatcgccgc--gtgcggttgctcttccccg-cttgatttgatg---ctgatttgggt-----tttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACGGGGCACGGGCACCGTCAAGCTTCTCAAGAACAAGGAGACCGGCAAGGTC
                | ||| ||   ||  | | | || |  | | || |     |  ||  |||| ||   ||  | ||| || ||   |||||  | |      ||||||||||||||||||| ||||||||||| || || |||||||| |||||||| ||||| ||||||||||||||||| |||||| ||||||||| ||||||||||
gtgagccccccccgccgccgccgcttgctctctctcctcttctcccctctcttgtagctcgtgtgctttttttcggttcgatctggtggcgctgatccgcgcgattgtttgcagGAAGGCGAAGCTTTACCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCGGGGGACGGGCACCGTCAAGCTCCTCAAGCACAAGGAGAACGGCAAGGTC

upper sequence: AC213884.3_FGT001 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G29410.1 (Glycine max), 3'ss of exon 1
gtgaggcgctgcccccttccccacttccttgctcatcgccgcgtgcggttgctcttccccgcttgatttgatgctgatttgggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACGGGGCACGGGCACCGTCAAGCTTCTCAAGAACAAGGAGACCGGCAAGGTC
      ||   || |   | |    ||  || || |    |  |    ||  | ||       ||| |||| |||  ||  | | ||  ||||||||||||||||| |||||||| || || |||||||| |||||||| || |||   || | ||| ||||| || ||  | ||||  ||||| ||||| 
---gtacgaaaccacacacacactctctctgttctt----gaattgattttgtgttttgaatgtgaattga-gcttgtt--gttgttatagGAAGGCGAAGCTGTATCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCGTGGCGGCGGGAACGTTAAGCTGCTGAAACATAAGGTCACCGGGAAGGTG
















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|21891716|gb|BQ744929.1|BQ744929
EST:     GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAATCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|211328842|gb|FK989029.1|FK989029
EST:     GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|30087993|gb|CB886198.1|CB886198
EST:     GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|211331008|gb|FK989048.1|FK989048
EST:     GAGGTACTCGTCACCACGGGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAATCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|30087992|gb|CB886197.1|CB886197
EST:     ACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
genomic: ACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|22472891|gb|BU037371.1|BU037371
EST:     GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAATCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|211330999|gb|FK989039.1|FK989039
EST:     GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|211328849|gb|FK989036.1|FK989036
EST:     GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAS-TGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|23357724|gb|BU645373.1|BU645373
EST:     GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAATCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|211330998|gb|FK989038.1|FK989038
EST:     GAGGTACTCGTCACCAC-GGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAATCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|211328838|gb|FK989025.1|FK989025
EST:     GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|22715361|gb|BU197722.1|BU197722
EST:     GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAATCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|211328846|gb|FK989033.1|FK989033
EST:     GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|211331000|gb|FK989040.1|FK989040
EST:     GAGGTACTCGTCACCAC-GGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGA
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGA
EST: gi|211331006|gb|FK989046.1|FK989046
EST:     AGGTACTCGTCACCACCGGT-AGGAAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCG-A-MTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
genomic: AGGTACTCGTCACCACCGGTGAGG-AGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|211328844|gb|FK989031.1|FK989031
EST:     GAGGTACTCGTCACCAC-GGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|211331001|gb|FK989041.1|FK989041
EST:     GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAA-CTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|211326678|gb|FK989021.1|FK989021
EST:     GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCCACAT                         GAAGGCGAAS-TGTACCGGTTTGATAAAGACGGGAAC-AATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|211331002|gb|FK989042.1|FK989042
EST:     GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAS-TGTNACCGGTTTGATAAAGACGGGAACCAATGGAAGGAAC
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGT-ACCGGTTTGATAAAGACGGGAACCAATGGAAGGAAC
EST: gi|211328843|gb|FK989030.1|FK989030
EST:     GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAATCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|211328848|gb|FK989035.1|FK989035
EST:     GAGGTACTCGTCACCAC-GGTGAGGAGGACGAGGACGTCCTGCTCGACAT                         GAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
genomic: GAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG
EST: gi|211331009|gb|FK989049.1|FK989049
EST:     GAGGACGTCCTGCTCGACAT                         GAAGGCGAMG-TGTACCGGTTTGATAAAGACGGGAATCAATGGAAGGAACG
genomic: GAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACG

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: 326

GGGAGGAAGAGGACACGGGTGCCCAGGTGGCCCCCATCGTGCGGCTTGAGGAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACGGGGCACGGGCACCGTCAAGCTTCTCAAGAACAAGGAGACCGGCAAGGTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 496

GGGAGGAAGAGGACACGGGTGCCCAGGTGGCCCCCATCGTGCGGCTTGAGGAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACGGGGCACGGGCACCGTCAAGCTTCTCAAGAACAAGGAGACCGGCAAGGTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 445

GGGAGGAAGAGGACACGGGTGCCCAGGTGGCCCCCATCGTGCGGCTTGAGGAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACGGGGCACGGGCACCGTCAAGCTTCTCAAGAACAAGGAGACCGGCAAGGTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 474

GGGAGGAAGAGGACACGGGTGCCCAGGTGGCCCCCATCGTGCGGCTTGAGGAGGTACTCGTCACCACCGGTGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgct ... ggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACGGGGCACGGGCACCGTCAAGCTTCTCAAGAACAAGGAGACCGGCAAGGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgccgcgtgcggttgctcttccccgcttgatttgatgctgatttgggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACGGGGCACGGGCACCGTCAAGCTTCTCAAGAACAAGGAGACCGGCAAGGTC
                                   tgctgat  putative branch site (score: 474)
                          ttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggcgctgcccccttccccacttccttgctcatcgccgcgtgcggttgctcttccccgcttgatttgatgctgatttgggttttgcagGAAGGCGAAGCTGTACCGGTTTGATAAAGACGGGAACCAATGGAAGGAACGGGGCACGGGCACCGTCAAGCTTCTCAAGAACAAGGAGACCGGCAAGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA