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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaggactttgatctttccgtgctaatatttgtacagaaatctcatcctgatgactgtcactgaatcactccattattgtgctatgcaacatttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG

Basic information

species Zea mays
transcript GRMZM2G039263_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039263_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 10
attaggactttgatctttccgtgctaatatttgtacagaaatctcat--------cctgatgactgtcactgaatc-actccattattgtgctatgcaacatt-tttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG
          || | |||  ||| |||| |||||| |   ||    |        ||||   ||||||  | ||||  ||  || | ||| | ||| || ||  ||||||||||| ||||||||||| || ||||| |||||||||||||| ||||| |||||||| ||||||||||| || |||||||||||||||
----------tggtgtttgtgtgttaatctttgtatatgtatgatgttgatgattcctggctactgtctttaaatctgctttatgactgttcaatggaatatcatttcagTACTTCGTTGAGGCTGGAGCAATTGCTGTAAGGCGTGTGCGTAAGGAGGATTTGCGCCATGTTGCCAAGGCTACTGGTGCAACTATG

upper sequence: GRMZM2G039263_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 10
attaggactttgatctttccgtgctaatatttgtacagaaatctcatcctgatgactgtcactgaat-cactccattattgtgctatgcaacatttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG
 ||  |   |||   ||    | |   |  || ||| ||    | |     |      | | |  || || |   || |     | |    | | ||||||||||||||||||||||| || ||||| ||||| |||||||| || || ||  |||| ||||||||||| || |||||||||||  ||
-ttttgtggttgtgtttaagatacatgttcttttactgatgaatgacataaaaagtcatgaatttatgcattttgttctgactatttaattcttgtttcagTACTTTGTTGAGGCTGGGGCAATTGCTGTAAGACGTGTGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTG

upper sequence: GRMZM2G039263_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA05G29870.1 (Glycine max), 3'ss of exon 10
-attaggactttgatctttccgtgctaatatttgtacagaaatctcatcctgatgactgtcactgaatcactccattattgt---gctatgcaacatt-tttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG
  || |   ||   | |||  |   |  | ||| ||| ||    | ||       |  |||| |||||   | |||| || |    ||||  |   || ||||||||||||||||||||||| || ||||| ||||| |||||||| || || ||  |||| ||||||||||| || |||||||||||  ||
attttgtggttctgtgtttaagatatgctcttt-tactga---ttaatggcataaaaagtca-tgaatttatgcatttttttctgactatttattcttgtttcagTACTTTGTTGAGGCTGGGGCAATTGCTGTAAGACGTGTGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTG

upper sequence: GRMZM2G039263_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 10
-------------------attaggactttgatctttccgtgctaatatttgtacagaaatctcatcctgatga--ctgtcactgaatcactccatt--attgtgctatgcaacattttt----cagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG
                   |||    || |  | |   | |       ||| |  || | ||   |   | ||    | |   ||  ||||   | |  ||| |  | |      |||||    ||||||||||| ||||| || || ||||| || |||||||||||||| |||||  |||| ||||||||||| || || || || ||| ||
gtgagaatgaaaaccaatgattttctctatcgtttacacataacttagtttttgaagtattcaagtttagttgcgtttatgtttggttcaccgtaatggattctcatttctcttgtttttatttcagTACTTTGTAGAGGCAGGAGCTATTGCTGTTAGGCGTGTGCGCAAAGAAGACATGCGTCATGTTGCCAAGGCGACAGGAGCGACTCTG

upper sequence: GRMZM2G039263_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 10
attaggactttgatctttccgtgctaatatttgtacagaaatctcatcctg-atgactgtcactgaatcactccat-tattgtg-ctatgcaa-catt-tttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG
    |   | | ||| | || || || |||   ||   |||  |  ||||  |||    | ||  | |  ||   | |||| || |||   ||   || || ||||||||||| |||||||| || ||||| || |||||||| || || || ||  |||| ||||||||||| || |||||||||||||||
----gttttgtaatcgtgccttgata-tatccatatgcaaagttgttccttcatgtggataacaaatttcctttttctattttggctacctaaatgttattccagTACTTTGTGGAGGCTGGGGCAATTGCTGTGAGGCGTGTTCGGAAAGATGACATGCGCCATGTTGCCAAGGCAACTGGTGCAACTATG

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|31406088|gb|CD484820.1|CD484820
EST:     GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG                         TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
genomic: GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
EST: gi|211163739|gb|FL337964.1|FL337964
EST:     GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG                         TACTTNGTTGAGGCTGGTGCGATWGCAGTAAGGCGTGTGCGCAAGGAAGAT
genomic: GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
EST: gi|211239408|gb|FL328610.1|FL328610
EST:     GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG                         TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
genomic: GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
EST: gi|211157236|gb|FL334269.1|FL334269
EST:     GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG                         TACTTTGTTGAGGCTGGTGC
genomic: GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGC
EST: gi|211149768|gb|FL359580.1|FL359580
EST:     GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTC-TTGAAG                         TACCTTGTTGAGGCTGGTGCGATTGC
genomic: GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGC
EST: gi|211469893|gb|FL096482.1|FL096482
EST:     GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG                         TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
genomic: GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
EST: gi|67021395|gb|CO450144.1|CO450144
EST:     GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG                         TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
genomic: GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
EST: gi|7238110|gb|AW573332.1|AW573332
EST:     GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG                         TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
genomic: GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
EST: gi|211195400|gb|FL324707.1|FL324707
EST:     GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG                         TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
genomic: GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
EST: gi|60343155|gb|DN210128.1|DN210128
EST:     GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG                         TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
genomic: GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
EST: gi|31440979|gb|CD510410.1|CD510410
EST:     GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG                         TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
genomic: GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
EST: gi|61119168|gb|DN560129.1|DN560129
EST:     GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG                         TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
genomic: GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
EST: gi|67018449|gb|CO447198.1|CO447198
EST:     GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG                         TACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT
genomic: GAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGAT

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: 726

AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 245

AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 212

AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAGgtgtgttttt ... catttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctgatgactgtcactgaatcactccattattgtgctatgcaacatttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG
 tcctgat  putative branch site (score: 212)
                                             catttttc  putative PPT
                                           aacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaggactttgatctttccgtgctaatatttgtacagaaatctcatcctgatgactgtcactgaatcactccattattgtgctatgcaacatttttcagTACTTTGTTGAGGCTGGTGCGATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGACATGTTGCCAAAGCCACTGGTGCAACTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA