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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttaccggcttgtgattctggttccatgtggtcctatctgtgtgtgtcgctgcagtttctgaagatcatcacttccttccatgttgaactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG

Basic information

species Zea mays
transcript AC217401.3_FGT002
intron # 8
splice site 3'
intron type U2

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|32856217|gb|CD995898.1|CD995898
EST:     GGGGCGTCCAATATTACT                         TTCAAAGGGATGGGGTGCAAATTGGACAGATG
genomic: GGGGCGTCCAATATTACTgtgagttacc ... aactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG
EST: gi|32832647|gb|CD972325.1|CD972325
EST:     TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACT                         TTCAAAGGAATGGCGTGCAAATTGGACAGATG
genomic: TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACTgtgagttacc ... aactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG
EST: gi|67013218|gb|CO441967.1|CO441967
EST:     TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACT                         TTCAAAGGAATGGCGTGCAAATTGGACAGATG
genomic: TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACTgtgagttacc ... aactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG
EST: gi|78075435|gb|DV503869.1|DV503869
EST:     TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACT                         TTCAAAGGAATGGCGTGCAAATTGGACAGATG
genomic: TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACTgtgagttacc ... aactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG
EST: gi|60351674|gb|DN218647.1|DN218647
EST:     TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACT                         TTCAAAGGAATGGCGTGCAAATTGGACAGATG
genomic: TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACTgtgagttacc ... aactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG
EST: gi|149013746|gb|EE043205.2|EE043205
EST:     TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACT                         TTCAAAGGAATGGCGTGCAAATTGGACAGATG
genomic: TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACTgtgagttacc ... aactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG
EST: gi|60340042|gb|DN207015.1|DN207015
EST:     TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACT                         TTCAAAGGAATGGCGTGCAAATTGGACAGATG
genomic: TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACTgtgagttacc ... aactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG
EST: gi|60394083|gb|DN226953.1|DN226953
EST:     TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACT                         TTCAAAGGAATGGCGTGCAAATTGGACAGATG
genomic: TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACTgtgagttacc ... aactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG
EST: gi|40336432|gb|CK370502.1|CK370502
EST:     TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACT                         TTCAAAGGAATGGCGTGCAAATTGGACAGATG
genomic: TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACTgtgagttacc ... aactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG
EST: gi|32834810|gb|CD974488.1|CD974488
EST:     TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACT                         TTCAAAGGAATGGCGTGCAAATTGGACAGATG
genomic: TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACTgtgagttacc ... aactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG
EST: gi|20507721|gb|BQ279747.1|BQ279747
EST:     TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACT                         TTCAAAGGAATGGCGTGCAAATTGGACAGATG
genomic: TCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACTgtgagttacc ... aactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG

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: 48 (upstream exon), 48 (downstream exon)
Score: 173

TTCGGGATCAATCAATATACTACATACTACATTGCAGATCAACAAACTCCTCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACTgtgagttacc ... aactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 65

TTCGGGATCAATCAATATACTACATACTACATTGCAGATCAACAAACTCCTCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACTgtgagttacc ... aactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG


Block sizes: 45 (upstream exon), 36 (downstream exon)
Score: 27

TTCGGGATCAATCAATATACTACATACTACATTGCAGATCAACAAACTCCTCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACTgtgagttacc ... aactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 135

TTCGGGATCAATCAATATACTACATACTACATTGCAGATCAACAAACTCCTCCGCAGGGACCACCGAGCTACTCGTCCGACTGGGGCGTCCAATATTACTgtgagttacc ... aactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttaccggcttgtgattctggttccatgtggtcctatctgtgtgtgtcgctgcagtttctgaagatcatcacttccttccatgttgaactttgcagTTCAAAGGAATGGCGTGCAAATTGGACAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG