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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtgtttgcagcttctgtatctccatttttctggaataagattaaaggcactaattgtgcttattcttttgataatgaccatgtttgttctccttcagCGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACAGCTCTTCCATCTCCTGGATGGTCATCAGATCACAT

Basic information

species Zea mays
transcript GRMZM2G043509_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043509_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os10g27230.3 (Oryza sativa), 3'ss of exon 11
-----------------tctgtgtttgca-gcttctgtatctccatttt------tctggaataagattaaaggcacta-------attgtgcttattcttttgataatgacc-atgtttgttctc---cttcagCGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACAGCTCTTCCATCTCCTGGATGGTCATCAGATCACAT
                 | | | | || | ||||   |||    |||||      || | ||  |  ||  | | | ||       | |||  | |  | ||| || ||| || |   ||| | ||    ||||||||| || ||| ||||||| || || |||||||||||||||||||||||||||||||||||||| || ||||| ||||||| |||||| || ||||| ||
gtcagttcctggaccagtttatatctgtatgctttgatattataattttgtagcttcagtaaacatcttttaaggattacacagctagtgtcatgaaacatttaatgatggcccacacttgctttcgtatttcagCGGATTCATTGTCAGTGGAGTCGTTGTTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACGGCCCTTCCTTCTCCTGAATGGTCTTCGGATCATAT

upper sequence: GRMZM2G043509_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA09G15980.2 (Glycine max), 3'ss of exon 10
tctgtgtttgcagcttctgtatctccatttttctggaataagattaaaggcactaattgtgcttattcttttgataatgaccatgtttgttctccttcagCGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACAGCTCTTCCATCTCCTGGATGGTCATCAGATCACAT
         |        || | |  ||  || ||  ||||   |||   |  || |  || | |   ||||   ||     |||  | |     ||||||||| || |||   ||||| |||||||||||  |  |||||||||| ||||| || || |||||||| ||||| || |||| |||||| |||||||||||
---------gtgagcatggtgt-tatatcattttg--ataaacataatatctgta-tcttgttcacaattttatgaagagatatgact-tgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTGCTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT

upper sequence: GRMZM2G043509_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA02G26620.2 (Glycine max), 3'ss of exon 10
tctgtgtttgcagcttctgtatctccatttttctggaataagattaaaggcactaattgtgcttattcttttgataatgaccatgtttgttctccttcagCGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACAGCTCTTCCATCTCCTGGATGGTCATCAGATCACAT
         |        || | |  ||  || ||  ||||  ||||   |  || |  || | |   ||||   ||     |||  | |     ||||||||| || |||   ||||| |||||||||||  |  |||||||||| ||||| || || |||||||| ||||| || |||| |||||| |||||||||||
---------gtgagcatggtgt-tatatcattttg--ataaacttaatatctgta-tcttggtcacatttttatgaaaagatatgact-tgtggtttcagCGGATTCATTGGTTGTGGAGTCATTATTGGAGTTACTGGATGAGGAGAGTTTGAGGAAGGACACAGCACTTCCTTCACCTGAATGGTCCTCAGATCACAT

upper sequence: GRMZM2G043509_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA03G36550.1 (Glycine max), 3'ss of exon 10
tctgtgtttgcagcttctgtatctccatttttctggaataagattaaaggcactaattgtgcttattcttttgataatgaccatgtttgttctccttcagCGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACAGCTCTTCCATCTCCTGGATGGTCATCAGATCACAT
  |||| |  |      |||     ||||  | ||  |||| ||| ||    || ||       ||| |||    | |||     |||||  |  ||||||||| || |||   ||||| ||||| ||||| || ||||||||||||||||| || ||||||||||| ||||| ||||||| |||||| || ||||| ||
-gtgtgatatcttgcaatgttatgtcattaatttg--ataa-atttaacatcctgatca-----attgtttatgaagtgataccttttgtgtt--ttcagCGGATTCATTGGTTGTGGAGTCATTGTTGGAGCTATTGGATGAGGAAAGTTTGAGGAAAGACACAGCACTTCCTTCTCCTGAATGGTCCTCTGATCATAT

upper sequence: GRMZM2G043509_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA19G39210.3 (Glycine max), 3'ss of exon 10
tctgtgtttgcagcttctgtatctc-catttttctggaataagattaaaggcactaattgtgcttattcttttgataatgaccatgtttgttct-ccttcagCGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACAGCTCTTCCATCTCCTGGATGGTCATCAGATCACAT
              |    |||||  || | || ||  || |  || ||     |||     | |  ||  ||| | ||||     | | || |   ||||||||| || |||   ||||| |||||  ||||  | ||||||||||||||||| || ||||||||||| ||||| ||||||| |||||| || ||||| ||
-------------gtgtgatatcttgcaatgttatgtcattaatttgaataatttaacat--cctgatcacttgtttatgaagtgatatcttgtgttttcagCGGATTCATTGGTTGTGGAGTCATTGCTGGAGTTATTGGATGAGGAAAGTTTGAGGAAAGACACAGCACTTCCTTCTCCTGAATGGTCCTCTGATCATAT

upper sequence: GRMZM2G043509_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 10
tctgtgtttgcagcttctgtatctccatttttctggaataagattaaaggca-ctaattgtgcttattcttttgataatgaccatg---tttgttctccttcagCGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACAGCTCTTCCATCTCCTGGATGGTCATCAGATCACAT
  |   ||    ||||   |       |||| |  |     | ||     || || |   | ||| ||| | || |||  |   ||   |||||| |  |||||||||| |  | |||||||| || || |||||||| |||||||| ||    || || || |||||||||||||||||||| | |||||| || ||||||||
gttaacttaagtgcttactttcaggggttttacgcgccagtgtttgctttcatctcagatttctttttcatctggtaagcaatttgctttttgttttgtttcagCGGACACGCTAACAGTGGAATCGTTGTTGGAACTGTTGGATGAAGAGTCCTTGAGGAAGGACACAGCTCTTCCATCTCCAGAATGGTCTTCTGATCACAT

upper sequence: GRMZM2G043509_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 10
------------------------------tctgtgtttgcagcttctgtatctccatttttctggaataagattaaaggcactaattgtgcttattcttttgataatgaccatgtttgttctccttcagCGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACAGCTCTTCCATCTCCTGGATGGTCATCAGATCACAT
                                | |   |  |  || | ||      |  |||     |    ||   | |  || |  || |||   || |   |   |  |  |||||  |  | |||| ||||| || || ||||| ||||| |||||||| ||||||||||| || || |||||||||||||| ||||| ||||| |  ||||| || ||||| ||
gtaatctttttcctacatgtcggtttgcatctttttcctatattttatttacacatgtgcttcatacttgtagtttgtgccgttattgatgtttaggattctctaataaataagatttgtggt--tccagCCGACTCTTTAACGGTGGAATCATTGTTGGAACTCTTGGATGAGGATAGCTTGAGAAAAGACACAGCACTTCCTTCTCCGGAGTGGTCCTCTGATCATAT

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|93013839|gb|EB639359.1|EB639359
EST:     AAATTGCACAAGAGATTTTACTGGAACTGTTGATTACATATTTTACACAG                         CGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTT
genomic: AAATTGCACAAGAGATTTTACTGGAACTGTTGATTACATATTTTACACAGgttggtgcat ... tctccttcagCGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTT
EST: gi|32807360|gb|CD959594.1|CD959594
EST:     AAATTGCACAAGAGATTTTACTGGAACTGTTGATTACATATTTTACACAG                         CGGACTCCCTGACAGTGGATTCGTTATTGGAACTTTTGGATGAGGAAAGTT
genomic: AAATTGCACAAGAGATTTTACTGGAACTGTTGATTACATATTTTACACAGgttggtgcat ... tctccttcagCGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaggcactaattgtgcttattcttttgataatgaccatgtttgttctccttcagCGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACAGCTCTTCCATCTCCTGGATGGTCATCAGATCACAT
                                      tgtttgttctccttc  CT-rich tract
                 ttattcttttgataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgtgtttgcagcttctgtatctccatttttctggaataagattaaaggcactaattgtgcttattcttttgataatgaccatgtttgttctccttcagCGGACTCCTTGACAGTGGATTCATTATTGGAACTTTTGGATGAGGAAAGTTTAAGAAAAGACACAGCTCTTCCATCTCCTGGATGGTCATCAGATCACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - tgtttgc
- - - - - - gcttctg
- - - - - - - - - - - - - - ttttctg
- - - - - - - - - - - - - - - - - -gaataaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt