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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctaccgccgatttgttccctgaactaaacacttattcttcagaatcccctaacaacaccaacttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTTGGGCGCCCGCGCCACACCGGTGTGATGGTGGGGATGGGGCAGAAGGATG

Basic information

species Zea mays
transcript GRMZM2G047055_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047055_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 1
gtaagct------accgccgatttgttccc-tgaactaaacacttattcttcagaatcccctaacaacaccaacttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTTGGGCGCCCGCGCCACACCGGTGTGATGGTGGGGATGGGGCAGAAGGATG
|||||||      | | | |  | ||| || |  ||  ||    |    |||    |  |  |||         || || ||||||||||||||||| || || || || ||||| |||||||||||||| || || ||||| |||||||||||||| ||||| || ||||| |||||||| |
gtaagctgtttggatctcagggtggtttccgtttaccgaaatgctgcatttcttggtagcaaaactgaggtggtttgtgtcagGCTGGGTTCGCCGGAGATGATGCGCCCAGGGCTGTCTTCCCCAGCATTGTCGGCCGCCCTCGCCACACCGGTGTCATGGTCGGAATGGGCCAGAAGGACG

upper sequence: GRMZM2G047055_T01 (Zea mays), 3'ss of exon 2
lower sequence: EDO98923 (Chlamydomonas reinhardtii), 3'ss of exon 1
------------gtaagctaccgccgatttgttccctgaactaaacacttattcttcagaatcccctaacaacaccaacttctg-------------gcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTTGGGCGCCCGCGCCACACCGGTGTGATGGTGGGGATGGGGCAGAAGGATG
            |   | |    | |   ||  ||| |  ||  |  |   || |||       ||| |      | |   |||             ||||||||| || || || || || |||||  | || || ||||||  |||||| || || || |||||||||||||||||||| |||||||| ||||||    
tccatttaacttgggcgttgggcctggcgtgggccccgcgctgca-gcgcgttgttcgagcaaacctgatgctggcgatcgctgtgtcgccgtgtccgcagGCTGGCTTTGCTGGTGATGATGCCCCTCGCGCTGTGTTCCCCTCCATCGTGGGCCGGCCCCGCCACACCGGTGTGATGGTCGGGATGGGCCAGAAG----

upper sequence: GRMZM2G047055_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------gtaagctaccgccgatttgttccctgaactaaacacttattcttcagaatcccctaac--aacaccaacttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTTGGGCGCCCGCGCCACACCGGTGTGATGGTGGGGATGGGGCAGAAGGATG
                       | | |  | | | | |||           ||       ||  |||      ||  ||   ||   ||| | | | |||||||| |||||| | ||||| |||||  |||| || |||||||||||||| ||||| ||| | |||||||| ||||||||||| ||||| ||||| || |
gcatagcactgtgcattataaaggcatgaaatcccagcttttgatggcattttattgttgaataattccaggcgccggaattgaatttcaattgccg-cagGCTGGTTTCGCCAGAGACGATGCCCCCCGGGCTGTTTTCCCCAGCATCGTGGGGCGGCCGAGGCACACCGGAGTGATGGTGGGCATGGGACAGAAAGACG

upper sequence: GRMZM2G047055_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 3
----------------------gtaagctaccgccgatttgttccctgaactaaacacttattcttcagaatcc---cctaacaacaccaacttctg-gcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTTGGGCGCCCGCGCCACACCGGTGTGATGGTGGGGATGGGGCAGAAGGATG
                       |  ||   |   |  | ||   || |  ||   |   || ||   ||| |      |||        | ||    ||||||||| ||||| || ||||| || ||  | || || ||||||||||| |||||||||||  | ||||| || |||||||| || ||||| |||||||| |
ctcttttgcatctttatttataatgggcagacattggat-gtagactaatttatg-atcaatcctctcgaaactgtgtttaattttggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GRMZM2G047055_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S198_154V6.3 (Physcomitrella patens), 3'ss of exon 2
---------------------gtaagctaccgccgatttgttc-cctgaactaaacacttattctt-cagaatcccctaaca-acaccaacttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTTGGGCGCCCGCGCCACACCGGTGTGATGGTGGGGATGGGGCAGAAGGATG
                           || |  |  ||  |    ||| | |  |||  | || |  ||  ||     | ||    |  | ||   ||||||||| ||||| || || ||||||||  | ||||| || || |||||||| || || ||| | ||||| ||||||||||| || ||||| |||||||| |
aaccttaacttgcgtaccctcaatttttatcatcacttcatctgtctggagttcacatctcttgtaacatgatgagtaatcacgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GRMZM2G047055_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S198_157V6.3 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------------gtaagctaccgccgat--ttgt-tccctgaactaaacacttattcttcagaatcccctaacaacaccaacttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTTGGGCGCCCGCGCCACACCGGTGTGATGGTGGGGATGGGGCAGAAGGATG
                                                                                                            |   || |  |  ||  | || || |||   |   |||  |  ||  | |||      |     |  | ||   ||||||||| ||||| || || ||||||||  | ||||| || || |||||||| || || ||| | ||||| ||||||||||| || ||||| |||||||| |
gtatgatattaactgttttgatgatgcatttgtattctccctatgtgatgaagtggcttgcaataaaatgcagttctaaagcatgtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacct--aaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GRMZM2G047055_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------gtaa-gctaccgccgat-ttgttccctgaactaaacacttattcttcagaat-------cccctaacaacaccaacttctg-gcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTTGGGCGCCCGCGCCACACCGGTGTGATGGTGGGGATGGGGCAGAAGGATG
               |   | |   |   ||  | |||     |||  |    |  | | |||||            |||        | ||    ||||||||| ||||| || ||||| || ||  | || || ||||||||||| |||||||||||  | ||||| || |||||||| || ||||| |||||||| |
caattcatgctataatggcgttcatgataatactattcaagtgacttcagttgtgctgtccagaacgaaaccgtgtttaattgtggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GRMZM2G047055_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------gtaagctac--cgccgatttgttccctgaactaaacacttat------tcttcagaatcccctaa---caacaccaacttctg----------gcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTTGGGCGCCCGCGCCACACCGGTGTGATGGTGGGGATGGGGCAGAAGGATG
                                                                              |||| |||   | |   |   ||   | |||| | || |||      ||| || ||| | | ||     | |  |  |   |          ||||||||| |||||||| ||||| |||||  |||| || |||||||||||||| ||||| ||| | |||||||| ||||||||||| ||||| ||||| || |
gtatgcatgcttaccgcatatacgactgtaattctcccatgcaaatcgagcatgctaacaatcgcgccttgcatttgctaaggtacattgtctgatcaatcatagtactatatacatatcggtcctctgcataatgcgcaaaatctgaaattaggtctggtttatttggcgcagGCTGGTTTCGCCGGAGACGATGCCCCCCGGGCTGTTTTCCCCAGCATCGTGGGGCGGCCGAGGCACACCGGAGTGATGGTGGGCATGGGACAGAAAGACG

upper sequence: GRMZM2G047055_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------gtaagctaccgccgat--ttgt-tccctgaactaaacacttattcttcagaatcccctaacaacaccaacttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTTGGGCGCCCGCGCCACACCGGTGTGATGGTGGGGATGGGGCAGAAGGATG
                        |   || |  |  ||  | || || |||   |   |||  |  ||  | |||      |     |  | ||   ||||||||| ||||| || || ||||||||  | ||||| || || |||||||| || || ||| | ||||| ||||||||||| || ||||| |||||||| |
gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacct--aaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

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|38687699|gb|CK144730.1|CK144730
EST:     CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|211074261|gb|FL177903.1|FL177903
EST:     CTGAGGATATCCAGCCCCTCGTCTGCKACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTT
EST: gi|211270540|gb|FL358782.1|FL358782
EST:     CTGAGGATATMCAGCMCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGC
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGC
EST: gi|211274215|gb|FL334361.1|FL334361
EST:     CTGAGGATATCCAGCCCCTCGTCTGCNACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCTCCGAGGG
genomic: CTGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtaagctacc ... cttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctgaactaaacacttattcttcagaatcccctaacaacaccaacttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTTGGGCGCCCGCGCCACACCGGTGTGATGGTGGGGATGGGGCAGAAGGATG
                              ccctaac  putative branch site (score: 2)
                                             cttct  putative PPT
               ttattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctaccgccgatttgttccctgaactaaacacttattcttcagaatcccctaacaacaccaacttctggcagGCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTTGGGCGCCCGCGCCACACCGGTGTGATGGTGGGGATGGGGCAGAAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG