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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgtatgtttttctttaattctcgatgttttttcgtactgcccctacgttctgtgttgagagatatatgcatgtccatgtagaccgcgctagcaaggttatt...

Basic information

species Zea mays
transcript GRMZM2G145258_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145258_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S92_47V6.2 (Physcomitrella patens), 5'ss of exon 2
CCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAA-GACTCTCGTATCCAGGACACAGGGTACCAGGgta-----tgtttttctttaattctcgatgttttttcgtactgcccctacgttctgtgttgagagatatatgcatgtccatgtagaccgcgctagcaaggttatt
 |||||||| |||||||| |||||||| |||||||||||     | ||||  |       | | ||||| |||||| ||  | |||||    || |||| |||        ||||| ||  ||| |    |||||||  |  |     |   || | | ||    ||| |  |    |   ||| |   |  || |||    ||  
TCCTTTCTCCAAGAAGGACTGGTATGATATCAAGGCACCCAATATCTTCA-CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGCACCAAGgttattgccattttttttctattttttccgttttttact--ttattttttattttatctttgaggattttcgatgatttttgttgtgtgt-ctcgcattcgta--

upper sequence: GRMZM2G145258_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S80_120V6.1 (Physcomitrella patens), 5'ss of exon 2
CCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCA-GTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgtatg----tttttctttaattctcgatgttttttcgtactgcccctacgttctgtgt-tgagagatatatgca----tgtccatgta-gaccgcgctagcaaggttatt------------------------------------
 |||||||| |||||||||||||||||||||||||| ||       |||| |     |   | | |||||||| || ||  |||||||   |||||||| |||| |    |  | ||       |||  || | | | |  || |  |   ||  |||   |   | |  | |||    ||     ||  ||  | | | | |   || |                                     
TCCTTTCTCGAAGAAGGATTGGTATGACATCAAGGCCCCCAACACCTTCACGCAGAAGTCGC-TGGGGAAGACCCTGGTGACCAGGACCGCGGGTACCAAGgtaagagcatgctgctgggtgggtcggggtgtgtgcatggtggcggtgaattgagtggacgtagggtgcacgcagcattgattgggtgcgaatgtggtggaagaattgtggggttgacgagaggggtgttgcgtggggcgcaacag

upper sequence: GRMZM2G145258_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S219_50V6.1 (Physcomitrella patens), 5'ss of exon 2
CCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgtatgtttttctttaattctcgatgttttttcgtactgcccctacgttctgtgttgagagatatatgcatgtccatgtagaccgcgctagcaaggttatt---
 |||||||| |||||||| ||||||||||||||||||||       ||||    |   ||  | ||||||||||||||  | |||||   ||| || | || |  |   |||| |  | ||  | | | |   || |     ||  |       |    | | |  |  | | | |   |    |  |       | |||   
TCCTTTCTCCAAGAAGGACTGGTATGACATCAAGGCACCCAACACCTTCACGCAGAAGAATTTGGGGAAGACTCTCGTCACTAGGACCGCGGGAACTAAGgcaattagctcttcagatgtct-tatatatatata-tatatatatatatatatatatatgttttgggtttcttcgttagggtttcatttttgtc-tcattggg

upper sequence: GRMZM2G145258_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S179_15V6.1 (Physcomitrella patens), 5'ss of exon 2
CCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGG-AAGACTCTCGTATCCAGGACACAGGGTACCAGGgtatgtttttctttaattctcgatgttttttcgtactgcccctacgttctgtgttgagagatatatgcatgtccatgta-gaccgcgcta-gcaaggttatt----------------------------------------
 |||||||| |||||||||||||||||||||||||| ||       ||||  |       | | ||| ||||| |||||  |||||||   |||||||| |||  |    |  || ||| |   | | ||||  |  |     |  |||   |   |   | | |||   || ||  ||| |      ||  |||    | |                                         
TCCTTTCTCCAAGAAGGATTGGTATGACATCAAGGCTCCTAACACCTTCA-CGCAGAAGTCGTTGGGGAAGACCCTCGTCACCAGGACGGCGGGTACCAAGgtgcgagggt--ttgattgtttgtttgtttttat-ttatttgtttgtttattaaagttgggtttatctctgacctggtatggttatactgtgcatttctgtaattagcttctgatgagaggttttgtttgtttgggtttcag

upper sequence: GRMZM2G145258_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S46_147V6.1 (Physcomitrella patens), 5'ss of exon 2
CCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgta------tgtttttctttaattctcgatgttttttcgtactgccc--ctacgttctgtgttgagagatatatgcatgtccatgta-gaccgcgctagcaaggttatt-------------------------------------------------
 || ||||| |||||||||||||||||||||||||||||       |||| |      ||| | || |||||||||||  |||||||   ||| || | |||       | |  |||| |   || |  ||||| |  |||   | |  || ||| | |||  ||      |     ||  ||| || ||  | | | |  | | | ||                                                 
TCCCTTCTCCAAGAAGGATTGGTATGACATCAAGGCACCCAATACTTTCACTCAAAAGAACTTGGGAAAGACTCTCGTGACCAGGACCGCGGGAACGAAGgtggggggttatgcttctctctctcgctctgtttgtgtgtatctctcgcctccgtcccgtggggatttgattgaagttggacatttatgagagagatggatacgcttttttcttttgtgaagttgtacacggaactgacgcgggtttggatgcgacag

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|211223878|gb|FL178492.1|FL178492
EST:     GTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGG                         ATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGAT
genomic: GTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgtatgttttt ... ctggttttagATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGAT
EST: gi|84977073|gb|DW475495.1|DW475495
EST:     GGAAGACTCTCGTATCCAGGACACAGGGTACCAGG                         ATTGCTTCTGAGGGTCTGAAGCACAGGGTCTTTGAGGTTTGCCTAGCTGAT
genomic: GGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgtatgttttt ... ctggttttagATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGAT
EST: gi|18384904|gb|BM418103.1|BM418103
EST:     GTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGG                         ATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGTTTATCTGAT
genomic: GTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgtatgttttt ... ctggttttagATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGAT
EST: gi|31357009|gb|CD441366.1|CD441366
EST:     TCCAGGACACAGGGTACCAGG                         ATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGAT
genomic: TCCAGGACACAGGGTACCAGGgtatgttttt ... ctggttttagATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGAT
EST: gi|67018238|gb|CO446987.1|CO446987
EST:     GTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGG                         ATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGAT
genomic: GTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgtatgttttt ... ctggttttagATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGAT
EST: gi|67042647|gb|CO468902.1|CO468902
EST:     GTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGG                         ATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGAT
genomic: GTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgtatgttttt ... ctggttttagATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGAT
EST: gi|211234191|gb|FL178563.1|FL178563
EST:     GTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGG                         ATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGAT
genomic: GTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgtatgttttt ... ctggttttagATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGAT

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), 49 (downstream exon)
Score: 4095

CCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgtatgttttt ... ctggttttagATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 3096

CCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgtatgttttt ... ctggttttagATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2259

CCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgtatgttttt ... ctggttttagATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1796

CCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgtatgttttt ... ctggttttagATTGCTTCTGAGGGTCTGAAGCACAGAGTCTTTGAGGTTTGCCTAGCTGATCTTCAGGGCGACGAGGATCAAGCTTACAGGAAAATCAGGCTCCGTGCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTTTCTCTAAGAAGGATTGGTATGACATCAAGGCACCGTCGGTGTTCAGTGTGCGCAACATCGGGAAGACTCTCGTATCCAGGACACAGGGTACCAGGgtatgtttttctttaattctcgatgttttttcgtactgcccctacgttctgtgttgagagatatatgcatgtccatgtagaccgcgctagcaaggttatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcccc