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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtacagttttctccaatatgatgataactaccatgtagattttgaacagctcagtctgctagcctcttatgctttgttcctttgcttgcatatccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAG

Basic information

species Zea mays
transcript GRMZM2G181151_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 3
gtgtgtacagttttctccaatatgatgataactaccatgtagattttgaacagctcagtctgctagcctcttatgctttgttcctttgcttgcatatc-catctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAG
                   |  || |  |   | |  |  | ||||| |||||   | |||| ||||   |||| ||  |    | |   | ||| |  | |||  |||||||||||||||| |||||||||||||||||| | ||||||||||||||||||||||| ||||| || |||||||| || ||||| ||||||||||||
-----------------gtacgtgctactg-ttcctctacaaattttcaacagactaatctggtagcaagttatactgagcatttctttcttcatgtaacttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACTCGCCGTGGCCAAGTTCTGGAAGTTGACGGTGAAAAGGCTGTTGTGCAG

upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 3
--------gt-gtgtacagttttctccaatatgatgataactacca--tgtagattttgaa---cagctcagtct-gctagcctcttatgctttgttcctttgct----tgcatatccatctat------agGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAG-
        || |||||    | | |    | || || | |   |    | || | |||| |      |||| |   | |  ||   |||  ||| |    |  ||    |  ||    ||| |       |||| || ||||  ||||| ||||| ||||| ||  | |||||||| || ||||| ||||| ||||| || ||||||||||| ||||| |||||||| ||| 
taacgagtgtagtgtaatactctatttgctttgttgcttatggcttattctaaagtttgcaacttttctcaatgaagatgaccaactattttttatgttatgactgagttttatgctgatcaactgcatcaggGACCCAAGTTTCAAGAGATTGTTAACATTCGCTTAGGAGATGGTACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGG

upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 3
------------gtgtg-tacagttttctccaatatgatgataactaccatgtagattttgaacagctcagtctgctagcc-tcttatgctttgttcctttgctt---gcatatcca-tctat-agGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAG
            ||||| |||   | | |    |||| | ||    |   | |  | |||   ||    ||    | | |  | || ||  ||||  |   | ||   ||  ||| | || || |||| || ||||  ||||| ||||| || || ||  | |||||||| || ||||| ||||| ||||| || ||||||||||| ||||| |||||||| |||
gtaatgactgtagtgtgatactcctctgtatgctatgcttattctaaaattttcaacttttctcaatgaagatgaccaactattttttgtgttgtgaccgagttttatgctgatcaactccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG

upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 3
gtgtgtacagttttct--ccaatatgat-gataactaccatgtagattttgaacagctcagtctgctagcctc-ttatgctttgttcctttgcttgcatatccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAG
||    |  || | ||     ||||  |  || | |    ||   ||||||     |||| | | ||    |   ||   ||| |   ||    || |  | ||||   |||| || || |  ||||| ||||| || || ||  | |||||||| || ||||| ||||| ||||| || || |||||||| |||||||||||||| |||
gtaatgatggtgtgctagttgatatttttaatgaattttctg-gtattttggttttctcaatattctgctgtgactaaagtttatattttatactgaaactgcatc---agGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG

upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgtacagttttctccaatatgatgataactaccatgtagattttgaacagctcagtctgctagcctcttatgctttgttcctttgcttgcatatccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAG
                      |  || |   | |||| |   | ||  | |        || |  | ||  |||  || | |   || |      | | ||| ||||| || || |||||||||||||| || ||||| ||||| ||||| || || || ||||||||||| || |||||||||||||| ||||||||||| |||
---------------------gtattggtg-tttccatctttctcttttataa-------tgttctcgtcccatgggtt-tcctgatgatactgctttcctctctagGGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG

upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 3
gtgtgtacagttttctccaatatgatgataactaccatgtagattttgaacagctcagtctgct-agcctcttatgctttgttcctttgcttgcatatccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAG
|| | | |    || |  | |||  | ||   | || |   ||||   |  |  ||  |||| | ||  |||  || |   |   |||  ||  |  | || |   |||| || || || ||||| ||||| || || ||  | |||||||| || ||||| |||||||||||||| ||||||||||| || ||||| |||||||||
gtat-tcctcacttatttagtatttttatttattcctttctgattcatatgatttccatctgttcagaatctattgatcaatgattttctttctaattgcacc---agGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG

upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 3
gtgtgtacagttttctccaatatgatgataactaccatgtaga-ttttgaacagctcagtctgctagcctctta-tgctttgttcctttgcttgcatatccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAG
||   |    |||| |   || |  |  |   |   ||  | | |||| |   |   |   ||  | |  |  | ||   || | || |   |    | |  |  |  ||| ||||| || || || ||||| || || || |||||||||||||| || || |||||||||||| | ||||||||||| || |||||||||||||||
gtagatttgcttttttgtcatttcttctttcttctaatacaaagtttttattggagtatagtgacacctacacactgagatgatactataactcttaaactgttca--gGGTCCAAAATATCAGGAGATTGTCAATATTCGCCTTGGAGATGGCACAACGCGACGTGGTCAAGTCTTAGAAGTTGATGGGGAGAAAGCTGTTGTGCAG

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|33102148|gb|CF062108.1|CF062108
EST:     GGACTGTATCTGGTGTGGCCGGGCCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACT
genomic: GGACTGTATCTGGTGTGGCCGGGCCTCTGGTTATCTTGGATAAAGTAAAGgtgtgtacag ... ccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACT
EST: gi|211182799|gb|FL070450.1|FL070450
EST:     GGACTGTATCTGGTGTGGCCGGGCCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACT
genomic: GGACTGTATCTGGTGTGGCCGGGCCTCTGGTTATCTTGGATAAAGTAAAGgtgtgtacag ... ccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACT
EST: gi|33100953|gb|CF060913.1|CF060913
EST:     GGACTGTATCTGGTGTGGCCGGGCCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACT
genomic: GGACTGTATCTGGTGTGGCCGGGCCTCTGGTTATCTTGGATAAAGTAAAGgtgtgtacag ... ccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACT
EST: gi|211182798|gb|FL070449.1|FL070449
EST:     GGACTGTATCTGGTGTGGCCGGGCCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACT
genomic: GGACTGTATCTGGTGTGGCCGGGCCTCTGGTTATCTTGGATAAAGTAAAGgtgtgtacag ... ccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACT
EST: gi|8367004|gb|BE049949.1|BE049949
EST:     CGACTGTATCTGGTGTGGCCGGGCCTCTGGCTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAAGAAATCGTAAACATCCGACTTGGAGATGGCACCACT
genomic: GGACTGTATCTGGTGTGGCCGGGCCTCTGGTTATCTTGGATAAAGTAAAGgtgtgtacag ... ccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACT
EST: gi|9953932|gb|BE640515.1|BE640515
EST:     GGACTGTATCTGGTGTGGCCGGGCCTCTGGTTATCTTGGATAAAGTATTG                         GGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACT
genomic: GGACTGTATCTGGTGTGGCCGGGCCTCTGGTTATCTTGGATAAAGTAAAGgtgtgtacag ... ccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACT
EST: gi|31664290|gb|CD573015.1|CD573015
EST:     GGACTGTATCTGGTGTGGCCGGGCCTCTGGTTATCTTGGATAAAGTAAAG                         GGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACT
genomic: GGACTGTATCTGGTGTGGCCGGGCCTCTGGTTATCTTGGATAAAGTAAAGgtgtgtacag ... ccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcagtctgctagcctcttatgctttgttcctttgcttgcatatccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAG
                                            tccatct  CT-rich tract
                                               atctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtacagttttctccaatatgatgataactaccatgtagattttgaacagctcagtctgctagcctcttatgctttgttcctttgcttgcatatccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT