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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatcaggatcatatatactagaaccgaccgcctgagaatagattggtggggaagaaacacccccaaataaacatgcttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCGACGATGCACATGAACCGGATGGATCGCGACGAGCACCTCTACACCGCGT

Basic information

species Zea mays
transcript GRMZM2G340224_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G340224_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g41270.1 (Oryza sativa), 3'ss of exon 5
------------gtaaggatcaggatcatatatactagaaccgaccgcctgagaatagattggtggggaagaaacacccccaaataaacatgcttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCGACGATGCACATGAACCGGATGGATCGCGACGAGCACCTCTACACCGCGT
                  | ||| |||||||  | | | ||    |     |||| |  ||       |  |||         ||      |        ||||| || || ||||| |||||||| ||||| ||||||||||||||||| |||||||||||||||||| |||||||  | || |||||||||||||||||||
gtaaggatagccacgcttaccagaatcatatggaattgtacttcacattc-agaaaactttcagacttacaaaatgtttgtggatttggggggaaaaaaacagGCTGATGCAGACGGCAACGGGACAATCGATTACGAGGAGTTCATCACTGCGACGATGCACATGAACAGGATGGACAGGGAGGAGCACCTCTACACCGCGT
















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|71425328|gb|DR806616.1|DR806616
EST:     ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCT                         GCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
genomic: ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
EST: gi|21481043|gb|BQ577726.1|BQ577726
EST:     ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCT                         GCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
genomic: ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
EST: gi|21330641|gb|BQ486022.1|BQ486022
EST:     CTCATGGAAGCT                         GCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
genomic: CTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
EST: gi|71765068|gb|DR963005.1|DR963005
EST:     AAGTCCAGCAGCTCATGGAAGCT                         GCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
genomic: AAGTCCAGCAGCTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
EST: gi|7304607|gb|AW600546.1|AW600546
EST:     AGCGAGGCCAAAGTCCAGCAGCTCATGGAAGCT                         GCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
genomic: AGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
EST: gi|86466802|gb|DY233172.1|DY233172
EST:     ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCT                         GCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
genomic: ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
EST: gi|50324131|gb|CO519257.1|CO519257
EST:     ACAAGGGCACCAAGCTGAGCGAGGCCGACGTCCAGCAGCTCATGGAAGCT                         GCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
genomic: ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
EST: gi|21480881|gb|BQ577564.1|BQ577564
EST:     ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCT                         GCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
genomic: ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
EST: gi|21390432|gb|BQ528481.1|BQ528481
EST:     ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCT                         GCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
genomic: ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
EST: gi|87154477|gb|DY399266.1|DY399266
EST:     ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCT                         GCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
genomic: ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
EST: gi|21330105|gb|BQ485486.1|BQ485486
EST:     ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCT                         GCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
genomic: ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
EST: gi|21390265|gb|BQ528314.1|BQ528314
EST:     AC-AGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCT                         GCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
genomic: ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
EST: gi|12046168|gb|BF728307.1|BF728307
EST:     ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCT                         GCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
genomic: ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
EST: gi|7216885|gb|AW563007.1|AW563007
EST:     ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCT                         GCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG
genomic: ACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCG

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 2 RNA-Seq libraries.


Block sizes: 41 (upstream exon), 9 (downstream exon)
Score: 2

CGACAGCAGCGGCACCATCACCGTGGACGAGCTGCGGAGAGGGCTGGCCAACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCGACGATGCACATGAACCGGATGGATCGCGACGAGCACCTCTACACCGCGT


Block sizes: 41 (upstream exon), 46 (downstream exon)
Score: 13

CGACAGCAGCGGCACCATCACCGTGGACGAGCTGCGGAGAGGGCTGGCCAACAAGGGCACCAAGCTGAGCGAGGCCGAAGTCCAGCAGCTCATGGAAGCTgtaaggatca ... ttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCGACGATGCACATGAACCGGATGGATCGCGACGAGCACCTCTACACCGCGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgagaatagattggtggggaagaaacacccccaaataaacatgcttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCGACGATGCACATGAACCGGATGGATCGCGACGAGCACCTCTACACCGCGT
                                 aaataaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggatcaggatcatatatactagaaccgaccgcctgagaatagattggtggggaagaaacacccccaaataaacatgcttgcgtgcagGCCGACGCCGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCGACGATGCACATGAACCGGATGGATCGCGACGAGCACCTCTACACCGCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA