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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaaaataaaactaaaaaaatactatttgcttagtgtttgtctattcatggatggaccaactcaactcgtaatctgacatttcttcacctcgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG

Basic information

species Zea mays
transcript GRMZM2G178822_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 5
gtatgaaaaataaaactaaaaaaatactatttgcttagtgtttgtctattcatggatggaccaactcaactcgtaatctgacatttcttcacctcgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG
                   |||  | ||| |    || | | | | |   ||   || |  ||    || || | ||  ||   | |      | |||| ||   |||||||||||| ||||||||||||||||| |||||||||||||| |||||||| |||||||| || ||
-----------------gtaaagtttctact-atctactttgtattttggcacatatagtacatactaagtcatgattggatgatcccct-ttttgccaacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG

upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA01G35190.2 (Glycine max), 3'ss of exon 7
------------------gtatgaaa---aataaaactaaaaaa-atactatttgcttagtgtttgtctattcatg--gatggaccaactcaactcgtaatctgacatttcttcacctcgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG
                  || ||  |   | |||   |   |   ||  | ||  || |   ||| |  ||| |||  ||||        ||       || |    | |   ||  || ||  ||  |||| ||||||||||||||||| |||||||||||||| ||  | || | |||||| || || ||  ||||
gtgagtgtctgactgggagtttgggactaactaatggtgtcatttatgttcttcactaacgctttctgcattgatgatgatgatgagtaccattctaccattttgtttattaacatttcccccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG

upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA09G34610.1 (Glycine max), 3'ss of exon 7
----gtatgaaaaataaaactaaaaaaatactatttgcttagtgtttgtctattcatggatggaccaactcaactcgtaatctgacatttcttca-------cctcgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG
    ||||   |  |   |||||     |  | | || |      |  |   ||| || || ||  |     | |   |  ||| ||||| || |       || | ||  ||  |||||||||||||||||||||| |||||||||||||| ||  | || | |||||| || || ||  ||||
gtgagtatctgat-tgggactaatggtgtcatttatgttcttcactaatgctttc-tgcattgatgatgatgagtaccatgctgccatttgtttattaactcccccccccccttctagATATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG

upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA16G08080.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------gtatgaaaaataaaactaaaaaaatactatttgcttagtgtttgtctattcatggatggaccaactcaactcgtaatctgacatttcttcacctcgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG
                                                      |  ||     || |    | | ||| |  ||    ||||| |    || | |    ||     | |  |||   | | | |||||| ||        |||||   ||||||||||||||||||||| |||||||||||| |||| || |||| |||||| || || ||  ||||
gtaagcatctgatattgaataattgccatttatggtgacttatgttttccaaaagattgtggtctagagtctagacaatgcatttcttgtagtgatgaattaatgacaagtg--ttgagt--actataagtttaacattttttt------tcatct-gcagATATGTGGGCAATGGGTGCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAG

upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA16G17580.1 (Glycine max), 3'ss of exon 7
-----------------------------gtatgaaaaataaaact----aaaaaaatactattt---gcttagtgtttg---tctattcatggatggaccaact-caactcgtaat--ctg-acatttcttcacctcgccatctc-atagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG
                              ||||   | | |   |    |||| | ||   | |   |  |||    ||   ||  |  |  |||| |   |   ||| |  | |   ||| |||||| |     | |     ||   ||||||||||||||||||||| |||||||||||| |||| || || | |||||| || |||||  ||||
gtgagcatctgatgttgaataattttcatttatggtgacttatgttttccaaaagattatggtctagagtctagacaatgcattccttgtagtgatgaattgatgacaagtgttgaatactgtacatttatcttttttgtttcatctgcagATATGTGGGCAATGGGTGCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAG

upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgaaaaataaaactaaaaaaatactatttgcttagtgtttgtctattcatggatggaccaactcaactcgtaatctgacatttcttcacctcgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG
          ||    |   || |||| | |  |  |  ||||  || || |  ||| | | |   |    | |||    |   ||  |    |     | |   |||||||||||| |||||||| || ||||| ||||||||| | || |  ||||||||||||||| | ||
--------gttagtcttcccaatataccaataacagaa-gttt--cttttta-agatagtctagtgcggtgcttaa--caatggttaatt--ttaattgtgtttcagATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTCTCTTTCCTGGAGCTAG

upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv09s0070g00320.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------gtatgaaaaataaaactaaaaaaatactatttgcttagtgtttgtctattcatggatggaccaactcaactcgtaatctgacatttcttcacctc--gccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG
                                       |   | || || ||     ||    || ||      | | | | ||||  |   | |   | | ||| |   ||  |  | || |  | ||| |   |   |    | |||||||||||||||||| | || ||||||||  |||| || |||| |||||||||||| ||      
gttacaaaagatgtaataaaaattgctgattttggtcttgctcggaagatcaattctcaa--ccaccatacaaagaatatgtctctacacgctggtat-cgagctccagAGGTTCTGCGTCAATCATCCACATATGGTTCTGCAGTCGATATGTGGGCAATGGGTACTATCATGGCTGAATTGTTTACTCTCCTTCCTCTCTTTCCAGG------

upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 7
gtatgaaaaataaaactaaaaaaatact--atttgcttagtgtttgtctattcatggatggaccaactcaactcgtaatctgacatttcttcacctcgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG
      |  ||| |  |  ||| | |||  | ||   |   |||||   |   ||  ||             | |  |    |  ||| ||  | |      |    ||||||||||||||||||||| || ||||||||  |||| || |||| |||||||||||| ||| | ||
---gtcagtatatagttggaaagagactgaaattttatgaagtttgaaaaaatatccatatttttgtctg--tagacactgaaattttatttccattttttccctccagATATGTGGGCAATGGGTGCTATCATGGCTGAATTGTTTACTCTCCGTCCTCTCTTTCCAGGATCGAG

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|60345317|gb|DN212290.1|DN212290
EST:     TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
EST: gi|31361016|gb|CD445373.1|CD445373
EST:     TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
EST: gi|67015254|gb|CO444003.1|CO444003
EST:     TCGGGCACCAGNAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
EST: gi|60352824|gb|DN219797.1|DN219797
EST:     TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
EST: gi|211493408|gb|FL041695.1|FL041695
EST:     TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTG                         ATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC
genomic: TCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTC

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: 261

GTATCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

GTATCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 145

GTATCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 296

GTATCGGGCACCAGAAGTCTTGCTCCAGTCATCTGCTTATGATTCTGCAGTTGgtatgaaaaa ... catctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggatggaccaactcaactcgtaatctgacatttcttcacctcgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG
                       atctgac  putative branch site (score: 296)
                               tttcttcacctcgcc  CT-rich tract
                              atttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaaaataaaactaaaaaaatactatttgcttagtgtttgtctattcatggatggaccaactcaactcgtaatctgacatttcttcacctcgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT