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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatctgactaactacttcgtcgaagtttttctcatattttttgtgccattattagataccatgatgataatagatcctgactttattttttgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTT

Basic information

species Zea mays
transcript GRMZM2G048277_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g24540.1 (Oryza sativa), 3'ss of exon 2
aatctgactaactacttcgtcgaagttttt---ctcatattttttgtgccatt-attagataccatgatgataatagatcctgactttattttttgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTT
      ||| ||   ||  | |  || | |   ||||   |  ||     |   | |||| || |||   |||   ||     | |    ||||  |||| ||| |||| ||||| || |||||||| ||||| || |||||||||||||||||||| |||||||||||||| || |||||||| ||||| ||||| ||||| |
----ccacttacatgttgcttgctgtctgtaggctcaggctgctttcataacccactagacactatgtatatatccgactgatattactattttgatactgcagATAGCCCAAGAATACTCTGAATGTCCATCTGGAAAGAAAGGTGGAGATCTTGGATGGTTCCCGCGTGGAAAAATGGCTGGCCCTTTTCAGGATGTTGCAT

upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G33180.2 (Glycine max), 3'ss of exon 3
-----aatctgactaactacttcgtcgaagtttttctcatattttttgtgccattattagataccatgatgataatagatcctgactttattttttgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTT
     |   | | |||  |  | ||  |   |||      | | |     | |  |||   | |||   || |  |  |||   |  || |   |      |||| |||| ||||||||||| ||||| || ||||| ||||| |||||||| ||||| ||||| || || || ||||||||||| || || ||||| ||||| |
ttgaaaggataaataagaatctggttca---tttgaaatcaatctagagacaaacatttttttccaatttgttgtt--atcaataacttttcactgacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGATGTTGCCT

upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G21080.1 (Glycine max), 3'ss of exon 3
aatctgactaactacttcgtcgaagtttttctcatattttttgtgccattattagataccatgatga--taatagatcctgactttattttttgtact--acagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTT
  |   |     ||  |    |||  | ||| | |    ||         |  | |||   ||   |  |  |   |    |   |||||     |||  ||||||||||||||||||||| ||||| |||||||| ||||| |||||||| ||||| ||||| || || || ||||||||||| || || ||||| ||||| |
--ttgaaaaggataaataa--gaatctgttcacttgaaattaacctagagacaaaatattttgtccaattggttattatcaatagtatttcactgacttcacagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCT

upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT1G26550.1 (Arabidopsis thaliana), 3'ss of exon 3
aatctgactaactacttcgtcgaagtttttctcatattttttgtgccattattagataccatga-tgataatagatcctgactttattttt-tgt------actacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTT
     ||| | ||||    |  |  |||   | | || | ||  |  ||   |   |   |||| |  |     ||| | ||   |||| | |||      |   ||| | |||  |||||| ||||| || ||||||||||| ||||| ||||||||||| |||||||| || || |||||||| ||||| ||||| || || || |
-----gac-atctacaagtttcagttttcggttagatatatttcg--atagatgtgtgttatgaattgtggagaatcttaacacgatttgtgtgtggaacgatctcagATTGCAGCAGAGTACTCTGAGTGTCCATCAGGGAAAAAAGGAGGAGATCTTGGATGGTTCCCTCGAGGAAAGATGGCAGGTCCATTCCAAGATGTCGCCT

upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g06430.t01 (Vitis vinifera), 3'ss of exon 3
-aatctgactaactacttcgtcgaagtttttctcatattttttg----tgccattattaga--taccatgatgataatagatcctgactttattttttgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTT
     |   |  | |  || ||  | |   |   |      | |    | |  || || ||  | |  |||| || ||   | ||  ||||||||| |      ||| |||||  ||| ||||| ||||| |||||||||||||| ||||| || ||||| ||||| ||||||||||||||||||||||| || ||||| ||||| |
ctgcatacatctccatctcatcacactaactgaaaagaagatagaaaattctcttcttggagttcctgtgataattattt-ttcttcctttattttct------cagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTTGGATGGTTTCCGCGTGGCAAGATGGCTGGTCCATTTCAGGATGTTGCCT

upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S217_91V6.1 (Physcomitrella patens), 3'ss of exon 3
aatctgactaactacttcgtcgaagtttttctcatattttttgtgccattattagataccatgatga---taatagatcctgactttattttttgtac-tacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTT
      |  || || | |  ||| |  || |  | |||| |    | | |      | |  ||  |    | |||  |  |   ||  |||| |   | | ||| ||||   ||| || || ||||| |||||||| |||||||| ||||| || || ||||| || ||||||||||||||||| |||||||||||||| || |
---accataaaatattgccacga-gcgttgcataaatttctgcatcgaatggcgttttcagtggagcatttcataatttgtagtttggttttgtactcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTCGGGTGGTTTCCTCGTGGCAAGATGGCTGGACCTTTCCAGGAGGTGGCCT

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|211235092|gb|FL220625.1|FL220625
EST:     ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAG                         GTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
genomic: ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAGgtaaggaccc ... tgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
EST: gi|6672235|gb|AW282401.1|AW282401
EST:     ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAG                         GTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
genomic: ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAGgtaaggaccc ... tgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
EST: gi|33096749|gb|CF056725.1|CF056725
EST:     TGGATGGCTGAATAATGGGGACCAAAGTTCCTCCTGCTGAGTTTGCTAAG                         GTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
genomic: TGGATGGCTGAATAATGGGGA-CAAAGTTCCTCCTGCTGAGTTTGCTAAGgtaaggaccc ... tgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
EST: gi|18179379|gb|BM380589.1|BM380589
EST:     ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAG                         GTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
genomic: ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAGgtaaggaccc ... tgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
EST: gi|211352278|gb|FL118750.1|FL118750
EST:     ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAG                         GTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
genomic: ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAGgtaaggaccc ... tgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
EST: gi|211107276|gb|FL481516.1|FL481516
EST:     ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAG                         GTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
genomic: ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAGgtaaggaccc ... tgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
EST: gi|40335959|gb|CK370029.1|CK370029
EST:     ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAG                         GTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
genomic: ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAGgtaaggaccc ... tgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
EST: gi|9731760|gb|BE510512.1|BE510512
EST:     ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAG                         GTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
genomic: ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAGgtaaggaccc ... tgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
EST: gi|60355788|gb|DN222761.1|DN222761
EST:     ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAG                         GTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
genomic: ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAGgtaaggaccc ... tgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
EST: gi|213169017|gb|FM182743.1|FM182743
EST:     GGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAG                         GTAGCACAAGAGTATGGTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
genomic: GGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAGgtaaggaccc ... tgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
EST: gi|5108029|gb|AI739742.1|AI739742
EST:     ATGGATGGCTGAATAATGGGGNCAAAGTTCCTCCTGCTGAGTTTGCTAAG                         GTAGCCCAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
genomic: ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAGgtaaggaccc ... tgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
EST: gi|211265808|gb|FL474211.1|FL474211
EST:     ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAG                         GTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT
genomic: ATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGAGTTTGCTAAGgtaaggaccc ... tgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattattagataccatgatgataatagatcctgactttattttttgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTT
                             tcctgac  putative branch site (score: 2)
                                   ctttatttttt  CT-rich tract
                                    tttattttttgtacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatctgactaactacttcgtcgaagtttttctcatattttttgtgccattattagataccatgatgataatagatcctgactttattttttgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG