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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccgccccgttaagtcgaagtctgggtgcatcttagtgtgttagtgtttgggcggtaacttgtgctatggtgtgattacacactgcggttaatactgtttctgacgcttgattttgcgctcctacttggtgctgttttttgtgcgacttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGATGCGCAGCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACA

Basic information

species Zea mays
transcript GRMZM2G069651_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069651_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g30412.1 (Oryza sativa), 3'ss of exon 1
gtaagtccgccccgttaagtcgaagtctgggtgcatcttagtgtgttagtgtttgggcg-gtaacttgtgctatggtgtgattacacactgcggttaatactgtttctgacgcttgattttgcgctcctacttggtgctgttttttgtgcgacttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGATGCGCAGCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACA
                                                        ||| ||||  |||   || ||||| |      |||  | |  ||| | |      | |||  |      | | |  ||     | | |  ||| |  |||||||||| ||||| || || ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||   ||||
--------------------------------------------------------gcgtgtaatctgt---atagtgtggtagtgtgctgatgcttttacagatctgtgtgtttgggtgatgaattcgatgtgacatgggtgt--gtgtggtttctgcagGCATTGGATAAGATTAGGTTCGAGAGCCTCACGGACAAGAGCAAGCTCGATGCGCAGCCGGAGCTGTTCATCCACATTGTCCCCGACAAGGCTAGCAACA

upper sequence: GRMZM2G069651_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S220_83V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagtccgccccgttaagtcgaagtctgggtgcatcttagtgtgttagtgtttgggcggtaacttgtgctatggtgtgattacacactgcggttaatactgtttctgacgcttgattttgcgctcctacttggtgctgttttttgtgcgacttctg-cagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGATGCGCAGCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACA
                                                       ||  ||  |      |    ||| |  |  |    | || | |  || || |    || || || |  ||| |      || |  |||  |   ||   ||| ||||| |||||||| || ||||| |||  ||| || |||||||||||| | |||| |||||| ||||||||||| || ||||| || ||||||||    ||||
-------------------------------------------------------ggacgtgccacaaaattgattgtcaaca-gcgaaacagtaatttatgcttgtatgactggagttggttctcatt-----tgttactttacgcttgagccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA

upper sequence: GRMZM2G069651_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S83_80V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagtccgccccgttaagtcgaagtctgggtgcatcttagtgtgttagtgtttgggcggtaacttgtgctatggtgtgattacacactgcggttaatactgtttctgacgcttgattttgcgctcctacttggtgctgttttttgtgcgacttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGATGCGCAGCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACA
                                         |||||  || |     |  | |  |||||  || ||||  |||     | | || | |  || | |||   ||| |      | |  |  ||    ||| || |||           ||||  ||||||| ||| | ||||||   || || |||||||||||||||||||  ||||| ||||| |||||||| ||  | || ||||||||    || |
-----------------------------------------tgtgtaggttt----actttgaaatgtgccgtgatgtgtctac-----gtgtttgaaagggtgt-tgagtgttgttgccatcccctgaactgtatttgtcttatgttt---------agGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGATGGCCAGCCAGAGCTCTTCATCCATATCATTCCCGACAAGGCGAACAATA

upper sequence: GRMZM2G069651_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ22362 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtccgccccgttaagtcgaagtctgggtgcatcttagtgtgttag-tgtttgggcggtaacttgtgctatggtgtgattacacactgcggttaatactgtttctgacgcttgattttgcgctcctacttggtgctgttttttgtgcgacttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGATGCGCAGCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACA
                                        | ||||||| || | |  |||  |    |  |    || |||| | ||  |   ||     | ||||||      |||||  | |   |  |||     ||| ||| ||||| |||  |||||  | ||||| ||  |||||||  | || ||||||||||||||||||||    ||||||||||| ||||||||||| || || ||||||||    || |
--------------------------------------gtgagtgttagatgctcgttcggcga----tatttcactgcgatt-ctcatcgatctttgccttctttctg-----cgatttctcaccgatctttg----cgttctttctgcgatttc--cagGCTCTCGACAAGATTCGGTTCGAAGGGCTGACTGACAAGAGCAAGCTCGAGAGCCAGCCGGAGCTTTTCATCCACATCGTTCCGGACAAGGCGAGCAAGA

upper sequence: GRMZM2G069651_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ25533 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtccgccccgttaagtcgaagtctgggtgcatcttagtgtgttagtgtttgggcggtaacttgtgctatggtgtgattacacactgcggttaatactgtttctgacgcttgattttgcgctcctacttggtgctgttttttgtgcgacttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGATGCGCAGCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACA
                                            || |||||| |           | | |||  |     ||  | |  || |   | |  | | |       |||||  | |   |  |||      || ||| ||||| |||  |||||  | ||||| ||| |||||||  | || ||||||||||||||||||||    ||||||||||| ||||||||||| || || ||||||||    || |
--------------------------------------------gtgagtgttagatgctcgttcggcgatattttactgctattctcatcgatctttgccttctttc---tgcgatttctcaccgatctttg----cattctttctgcgatttc--cagGCTCTCGACAAGATCCGGTTCGAAGGGCTGACTGACAAGAGCAAGCTCGAGAGCCAGCCGGAGCTTTTCATCCACATCGTTCCGGACAAGGCGAGCAAGA

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|211321100|gb|FL262984.1|FL262984
EST:     ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGAT                         GCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
genomic: ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgc ... acttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
EST: gi|211175291|gb|FL098027.1|FL098027
EST:     ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGAT                         GCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
genomic: ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgc ... acttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
EST: gi|211173626|gb|FL098026.1|FL098026
EST:     ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGAT                         GCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
genomic: ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgc ... acttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
EST: gi|211408945|gb|FK972015.1|FK972015
EST:     ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGAT                         GCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
genomic: ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgc ... acttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
EST: gi|211173623|gb|FL098023.1|FL098023
EST:     ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGAT                         GCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
genomic: ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgc ... acttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
EST: gi|211229546|gb|FL262944.1|FL262944
EST:     ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGAT                         GCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
genomic: ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgc ... acttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
EST: gi|211233673|gb|FL262968.1|FL262968
EST:     ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGAT                         GCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
genomic: ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgc ... acttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
EST: gi|211406934|gb|FK994254.1|FK994254
EST:     ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGAT                         GCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
genomic: ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgc ... acttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
EST: gi|211173613|gb|FL098013.1|FL098013
EST:     ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGAT                         GCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
genomic: ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgc ... acttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
EST: gi|211231622|gb|FL262964.1|FL262964
EST:     ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGAT                         GCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
genomic: ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgc ... acttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
EST: gi|211173614|gb|FL098014.1|FL098014
EST:     ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGAT                         GCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
genomic: ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgc ... acttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
EST: gi|211175292|gb|FL098028.1|FL098028
EST:     ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGAT                         GCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
genomic: ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgc ... acttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
EST: gi|32930417|gb|CF035229.1|CF035229
EST:     ATTCCGACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGAT                         GCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT
genomic: ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgc ... acttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgacgcttgattttgcgctcctacttggtgctgttttttgtgcgacttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGATGCGCAGCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACA
                                              cttctgc  CT-rich tract
       ttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccgccccgttaagtcgaagtctgggtgcatcttagtgtgttagtgtttgggcggtaacttgtgctatggtgtgattacacactgcggttaatactgtttctgacgcttgattttgcgctcctacttggtgctgttttttgtgcgacttctgcagGCGTTGGACAAAATCAGGTTCGAGAGCCTCACTGACAAGAGCAAGCTCGATGCGCAGCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT