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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtaccatcatattttccttgctttgcattattctgtaggtaccgaccttttcttatatcttgaaatttcataatacattgctctaatgacttatccttgtcaaattttttttactctagACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTTGCTCCATACTTGGAAGGGCTTAGCAGCACGCAGCTCCGCCTAGTAACCA

Basic information

species Zea mays
transcript GRMZM2G052078_T01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 20
gtcagtaccatcatattttccttgctttgcattattctgtaggtaccgaccttttcttatatcttgaaatttcataatacattgctctaatg-acttatccttgtcaaattttttttactctagACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTTGCTCCATACTTGGAAGGGCTTAGCAGCACGCAGCTCCGCCTAGTAACCA
                          |  ||   | || ||| |   |   |||    ||   |  |   ||| | || |||    |   |  |  | |  | ||    ||||  |   | ||||||||||| |||||  |||||||||||||||||||||||||||| ||||| |  || || ||||||||||||| |||||||||||| ||||| ||||| |
---------------------aaatgtctcaacctgctatagttcttgcattttcaccatgaatcaa---ttcgtgatgcatcatcccggttcatatctgatagtattgttttcatatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA

upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA13G19230.1 (Glycine max), 3'ss of exon 20
gtcagtaccatcatattttccttgctttgcattat---tctgtaggtaccgaccttttcttatatcttgaaatttcataatacattgctctaatgacttatccttgtcaaattttttttactctagACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTTGCTCCATACTTGGAAGGGCTTAGCAGCACGCAGCTCCGCCTAGTAACCA
                     |||||    ||| |     ||    | | | | ||||  |  ||  | ||||||     |   || |  || |  || ||  |     |||  |   |  |  |||| ||||| |||||||| |||||||| || |||||||||||||||||||||   ||||| |||||||| |||| |||||| ||| |     | || ||||
---------------------ttgctagaaattgtgggcatgcttttgctgtcatttttctccattctcaaattt---ggtctctttcattatt--ctcattttatgttaatggtggatggtacagACCGTTGTTTTCTGTCTAGTGGATATTTATATCATGCTTGGGAAAGCATTTTTGCCATATTTGGAAGGACTTAACAGCACACAGTTGAAGTTGGTCACCA

upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA19G35460.1 (Glycine max), 3'ss of exon 20
gtcagtaccatcatattttccttgctttgcattattctgtaggtaccgaccttttcttatatcttgaaatttcata-atacattgctctaatg-acttatccttgtcaaattttttttactctagACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTTGCTCCATACTTGGAAGGGCTTAGCAGCACGCAGCTCCGCCTAGTAACCA
                            | ||||   | |   |    ||   |  |||||| ||         || |||   || |  | |  ||||||  |    |||| |   ||  |  |||| ||||| |||||||| |||||||| || ||||||||||||||||||||    ||||| ||| ||||||||| |||||| ||| |     | || ||||
-------------------------agaggattagggtattatttatcactaataattatatttttgttccctttatatattctgtttcattatacttattttatataaatgtggattgttacagACCGTTGTTTTCTGTCTCGTGGATATTTATATCATGCTTGGGAAAGCATTCTTGCCATATTTGCAAGGGCTTAACAGCACACAGTTGAAGTTGGTCACCA

upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA10G04850.1 (Glycine max), 3'ss of exon 20
gtcagtaccatcatattttccttgctttgcattattctgtaggtaccgaccttttcttatatcttgaaatttc-ataa-tacattgctctaatgacttatccttgtcaaattttttttactctagACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTTGCTCCATACTTGGAAGGGCTTAGCAGCACGCAGCTCCGCCTAGTAACCA
                          ||||  ||   ||| || |      |  | | || | |    ||||| |||| |    |  | | ||   |     ||    |||  |   |  |  |||| ||||| |||||||| |||||||| || |||||||||||||||||||||   ||||| ||||||||||||| |||||| ||| |     | || ||||
-------------------------attgctataaattgttggcatgcttttgctgtaatttttctccatttccataactgttctcttttcatttttctcattttgttaatggtgcatggtacagACCGTTGTTTTCTGTCTAGTGGATATTTATATCATGCTTGGGAAAGCATTTTTGCCATATTTGGAAGGGCTTAACAGCACACAGTTGAAGTTGGTCACCA

upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA03G32710.1 (Glycine max), 3'ss of exon 20
gtcagtaccatcatattttccttgctttgcattattctgtaggtaccgaccttttcttatatcttgaaatttcataatacattgctctaatgacttatccttgtcaaattttttttactctagACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTTGCTCCATACTTGGAAGGGCTTAGCAGCACGCAGCTCCGCCTAGTAACCA
               | ||  ||       || ||| | |   |  |   | ||| ||    ||| | || |  |  | ||||  |||       |||  |    ||||     ||  |  |||| ||||| |||||||| |||||||| || ||||||||||||| ||||||    ||||| ||| ||||||||| |||||| ||| |     | || ||||
--------------gtattatttatcactaataattatatttttgtctgtcctttgttcc--ctttatatattctgtttcattattct-------tattttatgtaaatgcggattgttacagACCGTTGTTTTCTGTCTCGTGGATATTTATATCATGCTTGGGAGAGCATTCTTGCCATATTTGCAAGGGCTTAACAGCACACAGTTGAAGTTGGTCACCA

upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 20
lower sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 17
gtcagtaccatcatattttccttgctttgcattattctgtaggtaccgaccttttcttatatcttgaaatttcataatacattgctctaatgacttatccttgtcaaattttttttactctagACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTTGCTCCATACTTGGAAGGGCTTAGCAGCACGCAGCTCCGCCTAGTAACCA
        ||||||||   |   | | ||| | | |   |      | |||| | | |  || |  | |||| ||      ||  | || ||| ||||     |  | | | | ||     |||||||||| |||||||| ||||| ||||| ||||||||||||||||| |||   |||||| |||| ||||||| |||||| ||  | ||  | || || |
--------catcatatga-caaagttgtgcttaaatacatgatattctacctatgcatgcattt--atattttat------tttgtatattgatttatt----ttgagtctgtgttggc--agACTGTTGTATTCTGTCTAGTGGACATCTATATCATGCTTGGGAAAGCTTTTTTGCCATACCTGGAGGGGCTTAACAGCACACAATTGCGGTTGGTGACGA

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|87156618|gb|DY401407.1|DY401407
EST:     TGCCAGCATTATTTGATGCTTTTAACAACCAAAGTCCAGATGTCCGAAAG                         ACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTT
genomic: TGCCAGCATTATTTGATGCTTTTAACAACCAAAGTCCAGATGTCCGAAAGgtcagtacca ... tttactctagACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTT
EST: gi|26559542|gb|CA831777.1|CA831777
EST:     TGCCAGCATTATTTGATGCTTTTAACAACCAAAGTCCAGATGTCCGAAAG                         ACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTT
genomic: TGCCAGCATTATTTGATGCTTTTAACAACCAAAGTCCAGATGTCCGAAAGgtcagtacca ... tttactctagACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTT
EST: gi|32839431|gb|CD979112.1|CD979112
EST:     CAAAGTCCAGATGTCCGAAAG                         ACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTT
genomic: CAAAGTCCAGATGTCCGAAAGgtcagtacca ... tttactctagACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTT
EST: gi|32847553|gb|CD987234.1|CD987234
EST:     TGCCAGCATTATTTGATGCTTTTAACAACCAAAGTCCAGATGTCCGAAAG                         ACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTT
genomic: TGCCAGCATTATTTGATGCTTTTAACAACCAAAGTCCAGATGTCCGAAAGgtcagtacca ... tttactctagACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcataatacattgctctaatgacttatccttgtcaaattttttttactctagACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTTGCTCCATACTTGGAAGGGCTTAGCAGCACGCAGCTCCGCCTAGTAACCA
                ctctaat  putative branch site (score: 3)
                                        ttttttttactct  putative PPT
                                ttgtcaaatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtaccatcatattttccttgctttgcattattctgtaggtaccgaccttttcttatatcttgaaatttcataatacattgctctaatgacttatccttgtcaaattttttttactctagACTGTTGTGTTCTGTCTGGTGGATATCTACATCATGCTTGGGAAAGCATTTGCTCCATACTTGGAAGGGCTTAGCAGCACGCAGCTCCGCCTAGTAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC