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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacttcagctggaagaaacacaaatgtgttgtcttgaagcaatattaattgtgatgctatacagtttgaatcacttacttgatgggtatattgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG

Basic information

species Zea mays
transcript GRMZM2G135283_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 11
aacttcagctgg--aagaaacacaaatgtgttgtcttgaagcaatattaattgtgatgctatacagtttgaatcacttacttgatgggta------tattgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG
     ||||  |  | |||   |||||   | || ||  | ||  || |||||||   || ||   |||||| ||||| |||    |||       |||   |  |||||| |||   ||||||| || ||||| |||||||||||||||||||||||||||||  |||| ||||||||||  |||
-----cagcatgttacgaattgcaaattattggtttttcaacatgatgaattgtg---ctttaacatttgaaccacttccttatctggtggcaatttatcacttccagAGCTTGACAGCAAAAGGCTACGAACTTGTCTCTGGTGGGACTGACAACCATTTAGTGTTGGTAAATCTCAAGAGCAAG

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 11
------------------------------------------------aacttcagctggaagaaacacaaatgtgttgtcttgaagcaa-tattaattgtgatgctata-cagtttgaatcacttacttgatgggtatattgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG
                                                | |   | || |     ||  |   ||  | ||||  |  || | || |    ||   | |  |||||| ||       | |  || || | |     ||||||  || |   |||||| || ||||| || |||||||| |||||||||||||||||  |||||||  | |  || |||
gtaaaatgaatgccatttgtatgatgcacacaaatgctgtataaagccatcagaaactagttattacttagtagttgtatcttctactaaatgtttagccagacattttttcagttttaactgac--cctactgtgtttttgaacttcagAGTTTGTTAGAAAAAGGCTACGAACTTGTATCTGGTGGAACTGACAACCATTTAGTGTTGGTGAACTTAAGAAACAAG

upper sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT4G37930.1 (Arabidopsis thaliana), 3'ss of exon 11
aacttcagctggaagaaacacaaatgtgttgtcttgaagcaatattaat-tgtgatgctatacagtttgaatcacttacttgatgggtatattgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG
                   || |||    ||     ||| || |   || ||   |  |||  | ||||| |   |  ||  || | | | | ||   ||||  || ||    | |||||||||||| || |||||||| |||||||||||| | ||||| |||||||| |||   |||
-----------------gtactaatcccgtgaaggaaagaaaaacacatatggcgtagtatctactttgattatatctctacattgttgtttcgtg--cagACTCTAATGGAGAGAGGATATGAACTTGTTTCTGGTGGAACTGACAACCATCTGGTTCTAGTGAATCTAAAGCCCAAG

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|71299009|gb|DR785497.1|DR785497
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|108953686|gb|EC364842.1|EC364842
EST:     AGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: AGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|60353152|gb|DN220125.1|DN220125
EST:     GTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: GTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|6194529|gb|AW146633.1|AW146633
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|148928192|gb|EE284698.2|EE284698
EST:     ACAGAGCTTCCCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|166685188|gb|EG257794.1|EG257794
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCCGGTGGGACTGAC
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGAC
EST: gi|148973318|gb|EE024403.2|EE024403
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGTTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTTTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|60397906|gb|DN230722.1|DN230722
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|40336482|gb|CK370552.1|CK370552
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCCGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|148958251|gb|EC904465.2|EC904465
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|6102053|gb|AW126523.1|AW126523
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|60343439|gb|DN210412.1|DN210412
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|37393418|gb|CF633973.1|CF633973
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCCGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|60357206|gb|DN224179.1|DN224179
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|113700941|gb|EE678445.1|EE678445
EST:     CAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCCGGTGGGACTGACAACCAT
genomic: CAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|67013913|gb|CO442662.1|CO442662
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|60349820|gb|DN216793.1|DN216793
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|14204327|gb|BG838004.1|BG838004
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCCGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
EST: gi|60354435|gb|DN221408.1|DN221408
EST:     ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAG                         AGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT
genomic: ACAGAGCTTACCAAGAGCAAGTTATCAGTAATTGTGCTAAATTTGCGCAGgtatttgtgt ... ttgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattgtgatgctatacagtttgaatcacttacttgatgggtatattgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG
                                         tatattgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacttcagctggaagaaacacaaatgtgttgtcttgaagcaatattaattgtgatgctatacagtttgaatcacttacttgatgggtatattgttatcagAGCCTGATTTCAAAAGGATATGAACTCGTCTCTGGTGGGACTGACAACCATTTAGTTCTGGTGAATCTCAAGAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG