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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttcactatcggactgtactcatgtctactatctgatcatgtcaaagttctgacaattcttattattttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC

Basic information

species Zea mays
transcript GRMZM2G007276_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g38550.1 (Oryza sativa), 3'ss of exon 2
gtaagcttcactatcggactgtactcatgtctactatctgatcatgtcaaagttctgacaattcttattattttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC
||||||||  |||| |             ||||  || |    || ||||  |||| |||    |||| || || |||||| ||||||||| |||||||| || ||||||||||| |||||||||||||| ||||||||||  |||||||||||||| ||||||||||||||||| ||||| ||
gtaagctt-gctattga------------tctatgattttgctatatcaattttctaacagggtttataatgttcaattcttagTTTATCCTGATGGGCGCGTATGCATTTCTATCCTTCATCCACCTGGCGAAGATCCCAACGGTTATGAGCTTGCGAGCGAACGGTGGACACCTGTGCATAC

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G06960.1 (Glycine max), 3'ss of exon 3
gtaagcttcactatcggact-gtactcatgtctactatctgatcatgtcaaagttctgacaattcttattattttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC
|| ||  |   | | | | | ||  |  ||  |    |   |  |  | |||||       ||  ||  | ||     ||  |||| ||||| ||||| || |||||||| || ||||||||||| |||||||| ||||| | |||||| |||||||| || || || |||||||| || || ||
gttagtgttttttttgaatttgtgattttgctttgatttgaactacatgaaagt------gatgttttctgttcaatttttgcagTATATCCCGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTACGAGCTTGCGAGTGAGCGCTGGACACCTGTTCATAC

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 3
gtaagcttcactatcggactgtactcatgtctact---atctgatcatgtcaaagttctgacaattcttattatt-ttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC
             | ||  ||  ||||| | || |   ||||     ||    |    ||| |||   |  |  | ||  |||  |||| || || |||||||| |||||||| || |||||||||||||| ||||| || || | |||||||||||||||||| || || ||||| || || || ||
------------gttggtttg-gctcatttttatttttatcttgctttgattgatacatgataatgaatgatgctgttccatttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G14980.1 (Glycine max), 3'ss of exon 3
gtaagcttcactatc---ggactgtactcatgtctactatctgatcatgtcaaagttctga-caattcttattattttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC
|| || ||   | |        |||  |  ||  |        |  |  | |||||  | |   ||  ||  | ||     ||  |||| ||||| ||||| || |||||||| || ||||||||||| |||||||| ||||| | |||||||||||||||||| || || |||||||| || || ||
gttagtttttttttttttaatttgtgattttgctttgataggaacaacatgaaagtgatcagtgatgtttcctgttcaatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G40990.1 (Glycine max), 3'ss of exon 3
gtaagcttcactatcggactgtactcatgtctactatctgatcatgtcaaagttctgacaattcttattatt-ttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC
             | || ||| || ||| | |  ||||       |   ||    ||| | |   |  | || || ||||  |||| ||||| |||||||| |||||||| || ||||||||||| |||||||| || || | |||||||||||||||||| || || ||||| || || || ||
------------gttggtctg-acacattttttttatcctgcttcgattaatacatgaaattcaatgatgttgttcaatttgcagTGTATCCTGATGGGCGAGTTTGCATATCAATTCTTCATCCTCCTGGTGACGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT3G46460.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagcttcactatcggactgtactcatgtctactatctgatcatgtcaaagttctgacaattct-------tatt-attttgaattct-cagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC
|| || |         |  | | | |   |   ||   ||||| |||   |||    |   || |       | ||  | |||   ||| |||||||||| ||||| || ||||| || |||||||| ||||| |||||||| ||||| ||||| |||||||||||||| || || ||||| || || |||||
gttagttctttctctcggttatgcgctcattagctcattgatcttgtttgagtagctaaggttttgtgaaaatgttcgtcttgtggtctgcagTTTATCCCGATGGCCGCGTTTGTATATCTATTCTACATCCTCCTGGTGATGATCCAAGTGGATATGAGCTTGCAAGTGAGCGTTGGACGCCTGTTCACAC

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT5G59300.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------gtaagcttcactatcggactgtactcatgtctactatctgatcatgtcaaagttctgacaattcttattattttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC
                |  | ||    |||||       |       | |||      | | || |  | |||    | |  |||| ||       |||||||| | ||||| ||||||||||| |||||||||||||| || ||||| ||||| || |||||||||||||||||||| || ||||| || || || ||
gttagttttctctctatcggttttg--atcggggaaggattcaaaggaatatgaatagaagacagacgtttgaatggtttacttatatttgtcctgcagTTTATTCTGATGGTCGTGTTTGCATATCTATTCTTCATCCTCCCGGTGATGATCCTAGCGGTTATGAGCTTGCAAGCGAGCGTTGGACTCCTGTTCATAC

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT3G55380.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagcttcactatcggactgtactcatgtctactatctgatcatg--tcaaagttctgacaattcttattattttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC
|| |       |   |||   ||    | | |         | | |  | |   ||||||  |||  || | |||||| | |  ||||||| | |||||    ||||||||||||||||||||||| |||||||| |||||   ||| || ||||||||    ||||| ||||| || || || ||
gtgactgatttttctggaaaatatatctctttctcgagcttttaggatttagtcttctgatgatttatactcttttgactgc--agTTTATTCTGATGGAAAAGTTTGCATTTCTATTCTTCATCCTCCTGGTGATGATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATAC

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 3
---------gtaagcttcac-tatcggactgtactcatg--tctactatctgatcatgtcaaagttctgacaattcttattattttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC
          || || || | |||     | ||   |||  | |   ||  || ||        | || |   | | || | | || || |  |||||||||| ||||| || |||||||| || ||| | ||||| |||||||| || || | ||| |||||||||||||| || || |||||||| || |||||
gttaacttcttatgcctctcatatacatatatatatatgaatttctcattggagcactctctgatgctaattgtacctact-tcttaaactg-cagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGGACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACAC

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 3
---gtaagcttcactatcggactgtactcatgtctactatctgatcat---gtcaaagttctga--caattcttattattttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC
   |   | ||  | | | |  |||  |    | |    ||| | |||     ||  | |   |  ||| |    |  |     | |  |||||||||| ||||| || || ||||| || ||||| ||||| |||||||| || || | ||| |||||||||||||| || || ||||  ||| | || ||
gttggttgtttgtccaactgcatgtgtttgatttttgactcttaccattggagcatggcttgaaatcaacttggttcttgcatgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC

upper sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
lower sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
--------gtaagcttcactatcggactgtactcatgtctactatctgatcatgtcaaagttctgacaattcttatt----------attttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC
            | || ||| |  || || ||||||||    ||  |  || |  | | ||||||   |||   ||           | |||  ||   |||||||||| ||||| || ||||||||||| ||||| ||| | |||||||| ||||| | |||||||||  | || || || || ||| | || ||||| ||
gaaagaactctggtttgactct--gaatgcactcatgtgacttaatttttctttacgatgttctgcttatttccataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC

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|211084191|gb|FL360419.1|FL360419
EST:     CAACAGCCCGCCATCAGTAAGATTTACTTMTGGGATGTGGCATCCGAATG                         TTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAG
genomic: CAACAGCCCGCCATCAGTAAGATTTACTTCTGGGATGTGGCATCCGAATGgtaagcttca ... gaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAG
EST: gi|32840341|gb|CD980022.1|CD980022
EST:     CAACAGCCCGCCATCAGTAAGATTTACTTCTGGGATGTGGCATCCGAATG                         TTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAG
genomic: CAACAGCCCGCCATCAGTAAGATTTACTTCTGGGATGTGGCATCCGAATGgtaagcttca ... gaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAG
EST: gi|166597045|gb|EG301235.1|EG301235
EST:     CATCAGTAAGATTTACTTCTGGGATGTGGCATCCGAATG                         TTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAG
genomic: CATCAGTAAGATTTACTTCTGGGATGTGGCATCCGAATGgtaagcttca ... gaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctactatctgatcatgtcaaagttctgacaattcttattattttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC
                       ttctgac  putative branch site (score: 2)
                                                ttctc  putative PPT
                            acaattcttattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttcactatcggactgtactcatgtctactatctgatcatgtcaaagttctgacaattcttattattttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA