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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttttctccttcccttgccttgcacaccgttcggtgccatatcatggttgacttgactgagctgttaatcaatttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCAT

Basic information

species Zea mays
transcript GRMZM2G114126_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
gtgagtttt-ctccttcccttgccttgcacaccgttcggtgccatatcatggttgacttgactgagctgttaatcaatttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCAT
|| |||||| | ||||||||||   ||  ||  |     |   ||||| | ||||  |     || || ||||   |  | |||||||| |||||||||| ||||| ||||| || || ||||| || ||||||||||| ||||| |||||||| ||||| || |||||||||||||||||||| ||
gtaagttttgcaccttcccttg---tgagcaatgcc---tttaatatccttgttgttt-----gatcttttaacttaact-tttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT

upper sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G39880.1 (Glycine max), 3'ss of exon 4
------------------gtgagttttctccttcccttgccttgcacaccgttcggtgc-catatcatggttgacttgactgagctgttaatcaatttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCAT
                   |   | |||||  ||||| | ||    | | ||    ||  ||||   ||  ||   |   ||| ||   |    |||| || ||||  |||    | | ||  | ||||  || ||||| || ||||||||||| || ||||| || ||||| |||||||| || |||||||||||    |||| 
tgtaagcattactttcacatttttgttctctctccctcgtctccgtctctgtcatttgtgcatacattgcatggaat--ttgatcttacagattattt-ttgcaGCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCA-

upper sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 4
--------gtgagttttctccttcccttgc----cttgcacaccgttcggtgccatatcatggttgacttg-actgagctg-ttaatcaatttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCAT
         |   | ||||  || | |||      |||    |  |  ||    |  |  || ||   |   |||    |   | ||  | |  || ||||  |||||||| | || || |||||||| || || || || |||||||||||||| || ||||||||||||||||| ||||||| ||||||    || ||
tgttaattcttgttcttctaattacattgaagtatttgttagctttgtggatgtactttctgattatttcatactattataacttatttaatcattgcagCATCATGGGCTATATCTGTGTACTTCGCATACCAACGAACCTGGAAGCCTTTTAACCCTATCCTTGGAGAGACTTATGAGATGGCTAACCATGGTGGAAT

upper sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 4
-------gtgagttttctccttcccttgccttgcacaccgttcggtgcca-tat---catg---gttgacttgactgagctgttaatcaatttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCAT
       ||  |  ||||  |||      ||| |       | |  |  | |||   ||||    || | |       |   || ||  | |  |  ||||  |||||||  | ||||| ||||| ||||| || || || ||||||||||||||||| ||||||||||||||||| || |||||||||||    || ||
tccacttgttggagttcttgttcttcaatcttcctgttgcattgaagtaactataggcatgcgtatttattcagtgatgtactttatgtaatcatcacagCATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT

upper sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 4
-------gtgagttttctccttcccttgccttgc-acaccgttcggtgccatat---catg---gttgacttgactgagctgttaatcaatttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCAT
       ||  |  ||||  |||      ||| |     | ||   |    |||   ||||    || | |       |   || ||  | |  |  ||||  |||||||| | ||||| ||||| || || || || || ||||||||||||||||| ||||||||||||||||| || |||||||||||    || ||
gcttgttgttggagttcttgttcttcaatcttcctgttgcattgaataaactataggcatgtgtatttattcactgttgtactttatgtaatcatcacagCATCATGGGCTATATCGGTGTACTTTGCATACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT

upper sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S20_97V6.1 (Physcomitrella patens), 3'ss of exon 4
--------gtgagttttctccttcccttgccttgca------caccgttcggtgccatatcatggttgacttgactgagctgttaatcaatttgttt-cagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCAT
        || ||| |    ||| | |    ||| |       ||||||          |   || |    |   |   || ||  ||   |  ||| ||||||||||||| || ||||| |||||||| |||  ||| || ||||||||||| ||||| || || || ||||| || ||||||||  || |  | ||| |
atcacttcgtcagtgtatctcttgcttatgtttgtaaggaagtaccgttttacaagcagtggcggctactgttcttacactattg-tcgcctcatttgcagCTACATGGGCAGTATCGGTGTACTTCGCATATGCGCGGACCTGGAAGCCTTTCAATCCCATTCTCGGTGAGACCTATGAGATGGTCGACAAGAATGGCCT

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|211354689|gb|FL118768.1|FL118768
EST:     AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT                         CTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
genomic: AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTTgtgagttttc ... tttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
EST: gi|211354685|gb|FL118764.1|FL118764
EST:     AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT                         CTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
genomic: AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTTgtgagttttc ... tttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
EST: gi|71438648|gb|DR819698.1|DR819698
EST:     AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT                         CTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
genomic: AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTTgtgagttttc ... tttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
EST: gi|74236529|gb|DT644443.1|DT644443
EST:     AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT                         CTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
genomic: AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTTgtgagttttc ... tttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
EST: gi|26558339|gb|CA830574.1|CA830574
EST:     AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT                         CTACATGGGCT
genomic: AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTTgtgagttttc ... tttgtttcagCTACATGGGCT
EST: gi|211354686|gb|FL118765.1|FL118765
EST:     AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT                         CTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
genomic: AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTTgtgagttttc ... tttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
EST: gi|149105113|gb|EE290596.2|EE290596
EST:     AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT                         CTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
genomic: AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTTgtgagttttc ... tttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
EST: gi|148961873|gb|EE012659.2|EE012659
EST:     AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT                         CTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
genomic: AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTTgtgagttttc ... tttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
EST: gi|71329770|gb|DR801598.1|DR801598
EST:     AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT                         CTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
genomic: AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTTgtgagttttc ... tttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
EST: gi|87155561|gb|DY400350.1|DY400350
EST:     AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTT                         CTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT
genomic: AGACAAAGCAGATGAATGTGAGGATCCATACATGCGTATGGTTTATGCTTgtgagttttc ... tttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttcggtgccatatcatggttgacttgactgagctgttaatcaatttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCAT
                                   tgttaat  putative branch site (score: 3)
                                             tttgtttc  putative PPT
                                     ttaatcaatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttttctccttcccttgccttgcacaccgttcggtgccatatcatggttgacttgactgagctgttaatcaatttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG