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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagactatgaactatatcacctgccctttgtaacttgttatcccctgaacctactattttaccaatgacaggctactgttttcattccacacatgtttaaatttcataatttcaattgattttaacctatgcctcgtgctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATTGTGAAGCTGCTCGATATTGTTAGAGATCAGCATTCGAAAACGCCCAGCT

Basic information

species Zea mays
transcript GRMZM2G143602_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143602_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 2
-------gtagactatgaactatatcacctgccctttgtaacttgttatcccctgaacctactattttaccaatgacaggctactgttttcattccacaca------tgtttaaatttcataatttcaattgattttaacctatgcctcgtgctg-gtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATTGTGAAGCTGCTCGATATTGTTAGAGATCAGCATTCGAAAACGCCCAGCT
        |     |||||   | |   |   ||||| |   |  || |||||||||| | || ||||||   | ||| | |||||||| |||   ||||       ||| | |||  ||| | |     | |||||||||   |  |  |  ||  || ||||||||||||| || ||||| |||||||||||||||||||| || || || ||||| ||||| |||||||||||||||||||| || ||||| || ||||
gtagttcatgattcatgaatcctgttgtccatccttttt--ttccttttcccctgaacatgctcttttactggtaacatggtactgtttccatcttacacctagctttgtgtcaatggcattagtgtttattattttaaccatagttttcttttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATCGTGAAACTGCTTGATATTGTTAGAGATCAGCACTCAAAAACACCAAGCT

upper sequence: GRMZM2G143602_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 2
gtagactatgaactatatcacctgccctttgtaacttgttatcccctgaacctactattttaccaatgacaggctactgttttcattccacacatgtttaaatttca-taatttcaattgattttaacctatgcctcgtgctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATTGTGAAGCTGCTCGATATTGTTAGAGATCAGCATTCGAAAACGCCCAGCT
                                    | | |     ||    |  | |||   |  ||       | | |||  |    | ||   | |    |||| | |||     ||  |       |  ||| ||       ||||| ||||||||||| || || ||||||||| | |||||||| || || || ||||||||| | || ||||| ||||| ||||| || || || |||||  
------------------------------------tatgacgatttggcagtgatttttccgctttg------cattctttcgaactgatactaatctcttcttcacttattctggctgtctactgttcacaccttgt-------tagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC

upper sequence: GRMZM2G143602_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------gtagactatgaactat--atcacctgccctttgtaacttgttatcccctgaacctactattttaccaatgacaggctactgttttcattccacacatgtttaaatttcataatttcaattgattttaacctatg-cctcgtgctggt--gtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATTGTGAAGCTGCTCGATATTGTTAGAGATCAGCATTCGAAAACGCCCAGCT
                                          |    | |||| | |  |  |    |  ||| | | ||  |  |  | ||| |   || ||        | |   |  |    | ||||      | |  |||     |  | ||  |    |     | |     | |   | ||   |||||||||||||| || || ||||| || || ||||||||||| || |||||||||||||| || || |||||  | |||||||| ||||| || |||||| 
gtacctgactgctagtgatttttatggctggcgtcctagtttttagttgtgaagtttcaacaagtgacattttcttagttacttacatcagaaacagataattccttgggcagaacatctttaaataattcttacggtctgcaaaagatgtgttatctctgacctcatgtcaacaattttggatttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATTGTGAAGCTTCTGGACATTGTCCGTGATCAGCAATCGAAGACACCCAGCC

upper sequence: GRMZM2G143602_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 2
--gtagactatgaactata--------tcacctgccctttgtaacttgttatccc-----ctgaacctactattttaccaatg-------acaggctactgttttcattccacacatgtttaaatttcat-------aatttcaattgattttaacctatgcctcgtgctgg-----tgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATTGTGAAGCTGCTCGATATTGTTAGAGATCAGCATTCGAAAACGCCCAGCT
    ||| ||||  |||||        | ||  |   || || | |  || |  |     ||  |   | | |||| | || |       | || || |   ||         |     |||| |||  |       | | |   |    | ||| || ||  ||  ||||        ||||| ||||||||||| || ||  | |||||||| ||||||||||| || |||||||||||  | || ||||| ||||||||||| || ||||| |||||  
gtacagattatgg-ctatagttgggactgacaagaaattggttagtcattttggcaaaagctacagtcagtgttttgctaaagtctccatatagtctgcaagttgtggcgattatgcagttaatttttgttgagagtattcttgttctgatctaatctctggttctggctgcatcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC

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|211519092|gb|FL312014.1|FL312014
EST:     ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
EST: gi|211320448|gb|FL345953.1|FL345953
EST:     ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
EST: gi|23199704|gb|BU582269.1|BU582269
EST:     ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
EST: gi|211404409|gb|FL337659.1|FL337659
EST:     ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
EST: gi|32848629|gb|CD988310.1|CD988310
EST:     ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
EST: gi|211367442|gb|FL332752.1|FL332752
EST:     ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACMTT
genomic: ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
EST: gi|148979084|gb|EE026504.2|EE026504
EST:     ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
EST: gi|13388534|gb|BG462212.1|BG462212
EST:     ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
EST: gi|29576768|gb|CB616880.1|CB616880
EST:     ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
EST: gi|211328912|gb|FL338504.1|FL338504
EST:     ATAATGAGAAATGCATCATTAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
EST: gi|20507676|gb|BQ279725.1|BQ279725
EST:     ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
EST: gi|26560171|gb|CA832406.1|CA832406
EST:     ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
EST: gi|87156472|gb|DY401261.1|DY401261
EST:     ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
EST: gi|71770653|gb|DR968590.1|DR968590
EST:     ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAG                         ATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT
genomic: ATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 309

GGTCGGGAGAGGAAAATACAGTGAAGTATTTGAAGGTATTAATGTTAACAATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATTGTGAAGCTGCTCGATATTGTTAGAGATCAGCATTCGAAAACGCCCAGCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 273

GGTCGGGAGAGGAAAATACAGTGAAGTATTTGAAGGTATTAATGTTAACAATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATTGTGAAGCTGCTCGATATTGTTAGAGATCAGCATTCGAAAACGCCCAGCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 387

GGTCGGGAGAGGAAAATACAGTGAAGTATTTGAAGGTATTAATGTTAACAATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATTGTGAAGCTGCTCGATATTGTTAGAGATCAGCATTCGAAAACGCCCAGCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 203

GGTCGGGAGAGGAAAATACAGTGAAGTATTTGAAGGTATTAATGTTAACAATAATGAGAAATGCATCATCAAGATCCTCAAGCCTGTGAAGAAAAAGAAGgtagactatg ... gctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATTGTGAAGCTGCTCGATATTGTTAGAGATCAGCATTCGAAAACGCCCAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttaaatttcataatttcaattgattttaacctatgcctcgtgctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATTGTGAAGCTGCTCGATATTGTTAGAGATCAGCATTCGAAAACGCCCAGCT
                           ttttaac  putative branch site (score: 203)
     taaatttcataatttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagactatgaactatatcacctgccctttgtaacttgttatcccctgaacctactattttaccaatgacaggctactgttttcattccacacatgtttaaatttcataatttcaattgattttaacctatgcctcgtgctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATTGTGAAGCTGCTCGATATTGTTAGAGATCAGCATTCGAAAACGCCCAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA