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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagtattgaaggttctgatggtttcatatgcattattattacagctacttgtgctgtgggcatagttgaaattcatcccaaaatacagcaagctgtttagctttatcataagctagcagcctagcacagaagttggggaaataatatgtactcctgtgctgcagGTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGCTGATCTCTGGCCCAGGATTGCTAGCGCGGCAAATGCGATCGTCTAA

Basic information

species Zea mays
transcript GRMZM2G078396_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078396_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g56960.1 (Oryza sativa), 3'ss of exon 3
gtatagtattgaaggttctgatggtttcatatgcattattattacagctacttgtgctgtgggcatagttgaaat-tcatcccaaaatacagcaagctgtttagctttatcataagctagcagcctagcacagaagttggggaaataatatgtactcctgtgctgcagGTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGCTGATCTCTGGCCCAGGATTGCTAGCGCGGCAAATGCGATCGTCTAA-----------------
                                                |      ||| |   | |  ||||||| |  | | | || ||    |  ||  |||||| |  || |||  |   |||   |                |||||| ||| |  || ||||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||| || || ||||||||||||||||||                 
------------------------------------------------tgacca-gctatttcctttcttgaaatcttgtactacaaaactaataa-tgcatagcttcacgattagcctg--accttata----------------aatatgcacttccatgatgcagGTTCTGCCATCACTGGACCTATCGGAAAGGAGTGCGCTGATCTCTGGCCCAGGATTGCAAGTGCAGCAAATGCGATCGTCTAATCGAAGCAGCCATTGAA

upper sequence: GRMZM2G078396_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT3G04400.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatagtattgaaggttctgatggtttcatatgcattattattacagctacttgtgctgtgggcatagttgaaattcatcccaaaatacagcaagctgtttagctttatcataagctagcagcctagcacagaagttggggaaataa-tatgtactcctgtgctgc-agGTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGCTGATCTCTGGCCCAGGATTGCTAGCGCGGCAAATGCGATCGTCTAA-----------------
                                                                      ||| ||           |   |||      |  | |  | ||||   || ||  |   |   |  |   |   || | | |||  |    ||     ||| ||||| |||||||| || |||||||||||||| |||||||| ||||| || || || || || || || || ||||| |||                 
---------------------------------------------------------------------agaagtttgatatggggcaactcaaagccaatctcgtagtgataaatcagtagtatcatatttacttgtagctgatgagtctgttgtgtgatgtaattagGATCTGCTATCACTGGACCAATCGGAAAGGAGTGTGCTGATCTGTGGCCAAGAATCGCAAGTGCTGCGAACGCCATCGTTTAAGCAAGCTTGAGATCTCT

upper sequence: GRMZM2G078396_T03 (Zea mays), 3'ss of exon 4
lower sequence: PP1S280_69V6.1 (Physcomitrella patens), 3'ss of exon 3
--------gtatagtattgaaggttctgatggtttcatatgcattattattacag--ctacttgtgctgtgggcatagttg--aaattcatcccaaaatacagcaagctgtttagctttat-cataagctagcagcctagcacagaagttgggga---aataatatgtactcctgtg----ctgcagGTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGCTGATCTCTGGCCCAGGATTGCTAGCGCGGCAAATGCGATCGTCTAA-----------------
         |||     | ||   |||  ||   ||| || | || |    | ||  | | ||      || | ||  |||  | ||  ||  ||   ||       ||  |  |  |  |    | | ||  |   | |    ||   |   ||   | | ||| ||  |   |       |||||||||||| |||||||| || || || ||||||||||| ||| | ||||| ||||||||||| || || ||||| || |||| |                 
gtacgcagatatttccctcaaatatctt-tgacgtcagattcgttttagcaaaagatccagttagcgaatgagaatgattggcagatatatgtcatcgtatgttgttcttatcggaatgttgtgcacgttatgacttttgggatgagcctactgatttactgataggttttttggcaacttttgcagGTTCTGCTATCACTGGTCCTATTGGGAAGGAGTGCGCCGATTTGTGGCCTAGGATTGCTAGTGCTGCCAATGCCATTGTCTGAGGGCAATAGTTGTAATA

upper sequence: GRMZM2G078396_T03 (Zea mays), 3'ss of exon 4
lower sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatagtattgaaggttctgatggtttcatatgcattattattacagctacttgtgctgtgggcatagttgaaattcatcccaaaatacagcaagctgtttagctttatcataagctagcagcctagcacagaagttggggaaataatatgtactcctgtgctgcagGTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGCTGATCTCTGGCCCAGGATTGCTAGCGCGGCAAATGCGATCGTCTAA-----------------
                         |   | |          | ||  |  | |||| ||  ||| | | | |  |   || |       |   |  || ||||| ||   |      |  |  | ||| ||  | || ||   |  |  ||  |  |    ||||||||||||||||||||| || ||||| ||||||||||| ||  | ||||| |||||||| ||||| || || ||||| || | |                 
------------------------gtgagtgtatgcagccggtgca-ttgatggtgcagtctgcagattggga--tgggcctagg----gggggggggtatagctgtaaggtggag-ggtggattggcagagctgatgaggg--ttgtgcgtggttgtaatgtgcagGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT

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|166619421|gb|EG260150.1|EG260150
EST:     CCAAAGGGAGAGATGAAAG                         GTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGCTGATCTCTGGCCCA
genomic: CCAAAGGGAGAGATGAAAGgtatagtatt ... tgtgctgcagGTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGCTGATCTCTGGCCCA
EST: gi|113852970|gb|DW973271.1|DW973271
EST:     GTGAACCCAAAGGGAGAGATGAAAG                         GTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGCTGATCTCTGGCCCA
genomic: GTGAACCCAAAGGGAGAGATGAAAGgtatagtatt ... tgtgctgcagGTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGCTGATCTCTGGCCCA
EST: gi|113670582|gb|DW820560.1|DW820560
EST:     ACAATGCTGGAGTGATTGTGAACCCAAAGGGAGAGATGAAAG                         GTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGC
genomic: ACAATGCTGGAGTGATTGTGAACCCAAAGGGAGAGATGAAAGgtatagtatt ... tgtgctgcagGTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGC
EST: gi|166452992|gb|EG260614.1|EG260614
EST:     GTGATTGTGAACCCAAAGGGAGAGATGAAAG                         GTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGCTGATCTCTGGCCCA
genomic: GTGATTGTGAACCCAAAGGGAGAGATGAAAGgtatagtatt ... tgtgctgcagGTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGCTGATCTCTGGCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagctagcagcctagcacagaagttggggaaataatatgtactcctgtgctgcagGTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGCTGATCTCTGGCCCAGGATTGCTAGCGCGGCAAATGCGATCGTCTAA
                                       tactcct  CT-rich tract
                             aaataatatgtact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagtattgaaggttctgatggtttcatatgcattattattacagctacttgtgctgtgggcatagttgaaattcatcccaaaatacagcaagctgtttagctttatcataagctagcagcctagcacagaagttggggaaataatatgtactcctgtgctgcagGTTCTGCCATCACTGGGCCCATCGGAAAGGAGTGCGCTGATCTCTGGCCCAGGATTGCTAGCGCGGCAAATGCGATCGTCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT