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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacatttcttccattcgtcagatttcgtaacaggagaattcttccaacaaaattctctgttctgttccattgtgctctgctgtcattaaacacgatcaagttaccatttccatgcactctttatctgctgactgtcgtttgtctggtggatacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAGGCATGCC

Basic information

species Zea mays
transcript GRMZM2G107101_T04
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107101_T04 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g08700.2 (Oryza sativa), 3'ss of exon 14
gtgacatttcttccattcgtcagatttcgtaacaggagaattcttccaacaaaattctctgttctgttccattgtgctctgctgtcattaaacacgatcaagttaccatttccatg-cactctttatctgctgactgtcgtttgtctgg--tggatacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAGGCATGCC
                                               ||||   |  |   |   || |  ||  |  |   |  || | || |  |   ||||    |||  |||   |   |    | ||||| |     | || ||      |||  ||||||  ||||||| |||||  | || |||||||| ||| |||||||||||||||||||| |||| || || ||||| || || ||||||||||||       
---------------------------------------------gtaacaccttcattcatgaggtcc--ttaggtgcaaatcccagtgaagaataatcagttctactttgtatggttcatctcgcttactgaccggttcatctcgggatcaattacgagcagCTATTGGAAGTAACCGCCAGAGCAGTCCATCTCATCGTCGAATGGGGAGATTCAGGTGTATCCGTCGCTGATGGCCTCTCCAATCTGCTGAAG-------
















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|13315954|gb|BG410302.1|BG410302
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAG-GACCGCTCGGGCTG
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTG
EST: gi|13490512|gb|BG517276.1|BG517276
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|37397716|gb|CF636166.1|CF636166
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|91873510|gb|EB403467.1|EB403467
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|67013730|gb|CO442479.1|CO442479
EST:     CCGATGGAATGCTCGTNGATGGTGAAGCTTGTCCTTTGCCACAGCTTGAG                         CTCCTGGAA-TGACCGCTCGGGCTGTCC
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCC
EST: gi|40336821|gb|CK370891.1|CK370891
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAAT---GAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|40337172|gb|CK371242.1|CK371242
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|211306980|gb|FL381266.1|FL381266
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
EST: gi|211167624|gb|FL375018.1|FL375018
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTC-ATCTTACCATCGAATGGGGAGA
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGA
EST: gi|211533313|gb|FL400718.1|FL400718
EST:     CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAG                         CTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT
genomic: CCGATGGAATGCTCGTCGATGGTGAAGCTTGTACTTTGCCACAGCTTGAGgtgacatttc ... atacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttccatgcactctttatctgctgactgtcgtttgtctggtggatacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAGGCATGCC
                     tgctgac  putative branch site (score: 2)
             tctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgacatttcttccattcgtcagatttcgtaacaggagaattcttccaacaaaattctctgttctgttccattgtgctctgctgtcattaaacacgatcaagttaccatttccatgcactctttatctgctgactgtcgtttgtctggtggatacatgcagCTTCTGGAAGTGACCGCTCGGGCTGTCCATCTTATCATCGAATGGGGAGATTCAGGTTTATCAGTTGCAGATGGTCTTTCAAATCTGCTGAAGGCATGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG