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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaacgttgctgattgcaatacttgcaggacaggcatgtgtactacacaagtaaaccctagttttatctggccttttctcatcctttgttctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAGTATTGAAGAGAAACTATGGGCCAGAAATAGACATATGGAGTGCGGGAGT

Basic information

species Zea mays
transcript GRMZM2G311220_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G311220_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g61590.1 (Oryza sativa), 3'ss of exon 1
tagaacgttgctgattg--caatacttgcaggacaggcatgtgtactacacaagtaaaccctagttttatctggccttttctcatcctttgttctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAGTATTGAAGAGAAACTATGGGCCAGAAATAGACATATGGAGTGCGGGAGT
| ||       || |||  ||| | ||| |     |   | |||| |||| |   ||  |||||||  |||  | | ||         || |  |  ||||||||| |||||||| ||||||||||||||||| |||||||||||||| || |||||||||||||||||||| || |||||||| || |||||||| |||||
tggactcacagtgcttgtacaacagttg-atcgttgttctttgta-tacagacaaaactcctagttccatccagtccttatgtgattgttatgttcttttagGTGAGAAGTTTTCTGAAATTGTGGGAAGCCCATATTACATGGCTCCAGAGGTATTGAAGAGAAACTATGGTCCGGAAATAGATATTTGGAGTGCAGGAGT

upper sequence: GRMZM2G311220_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA18G43160.1 (Glycine max), 3'ss of exon 3
--tagaacgttgctgattgcaatacttgcaggacaggcatgtgtactacacaagtaaaccctagttttatctggccttttctcatcctttgttctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAGTATTGAAGAGAAACTATGGGCCAGAAATAGACATATGGAGTGCGGGAGT
    |     |  || || | | | ||  |   ||  | | |  | | |  |    | |     |||| ||      ||     |  | |       |  |||||| | ||| ||||||||||| ||||| || ||||| |||||||| |||||  | ||| | || ||||| ||||||||||| ||||||||||| |||||
tgctgtctactcatg-tttcgaca-ttatatttcaatctttttcattgcttacagtatctgacattttttccatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCAGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT

upper sequence: GRMZM2G311220_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 1
tagaacgttgctgattgcaatacttgcaggacaggcatgtgtactacaca-agtaaacccta-gttttatctggccttttctca-tcctttgttctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAGTATTGAAGAGAAACTATGGGCCAGAAATAGACATATGGAGTGCGGGAGT
     | |   | | |   | | ||  |   ||  | | |  | | |  | ||||      |  ||||   |    | || |   |  | |       |  |||||| | ||| ||||||||||| ||||| || ||||| |||||||| |||||  | ||| | || ||||| ||||||||||| ||||||||||| |||||
---ctcatgtttcactttcaaaattatatttcaatctttttcattgcttacagtatctgacatattttccataatgtgttgtgggtaatataaaaatttccagGTGAGAGGTTCTCAGAAATTGTTGGAAGTCCATATTATATGGCTCCGGAAGTGCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT

upper sequence: GRMZM2G311220_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 1
tagaacgttgctgattgcaatacttgcaggacaggcatgtgtactacacaagtaaaccctagttttatctggccttttctcatcctt----tgttctactt-tagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAGTATTGAAGAGAAACTATGGGCCAGAAATAGACATATGGAGTGCGGGAGT
      |||||        ||  |      | | |  ||  || |   || |     | || ||  | |||    | ||| || |||    | ||  |||| ||||||| | ||| || |||||||| ||||| || |||||||||||||| || ||  | ||| | || ||||| ||||||||||| ||||||||||| |||||
----tagttgcaaggctttatcttatttaaataagtttgc-taatctgcatgagtttcatatttccagctgatactatctaatgcttaaattcttgaacttctagGTGAGAGGTTCTCTGAAATTGTTGGAAGTCCTTATTACATGGCTCCAGAGGTCCTCAAGCGGAATTATGGACCAGAAATAGATATATGGAGTGCAGGAGT

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|149085145|gb|EE174649.2|EE174649
EST:     CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTG                         GTGAAAAAGTTTTCAGAAATTGGTGGGAAGCCCCTATTACATGGCTCCTGA
genomic: CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcaca ... tctactttagGTGAAAA-GTTTTCAGAAATTG-TGGGAAGCCCCTATTACATGGCTCCTGA
EST: gi|149102142|gb|EE287576.2|EE287576
EST:     CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTG                         GTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAG
genomic: CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcaca ... tctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAG
EST: gi|21432179|gb|BQ547669.1|BQ547669
EST:     CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTG                         GTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAG
genomic: CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcaca ... tctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAG
EST: gi|149113217|gb|EE288137.2|EE288137
EST:     CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTG                         GTGAAAAAGTTT-CAGAAATTGTGGGGAAGCCCCTATTACAT
genomic: CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcaca ... tctactttagGTGAAAA-GTTTTCAGAAATTGTGGG-AAGCCCCTATTACAT
EST: gi|71774878|gb|DR972756.1|DR972756
EST:     CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTG                         GTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCT
genomic: CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcaca ... tctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCT
EST: gi|78118424|gb|DV536810.1|DV536810
EST:     CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCTATCTTCTTCAAGCCTG                         GTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAG
genomic: CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcaca ... tctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacaagtaaaccctagttttatctggccttttctcatcctttgttctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAGTATTGAAGAGAAACTATGGGCCAGAAATAGACATATGGAGTGCGGGAGT
                           ccttttctcatccttt  CT-rich tract
              tagttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaacgttgctgattgcaatacttgcaggacaggcatgtgtactacacaagtaaaccctagttttatctggccttttctcatcctttgttctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAGTATTGAAGAGAAACTATGGGCCAGAAATAGACATATGGAGTGCGGGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - gttgctg
- - - - - - - - - - tacttgc
- - - - - - - - - - - - - - - - aggcatg
- - - - - - - - - - - - - - - - - - - - - -ctacaca