Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
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 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtacggtatatatatgggatccatcttcttctccaattccacaatctcatcgtttcagtctgcttccatcactcatgctactagttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG

Basic information

species Zea mays
transcript GRMZM2G300348_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G300348_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g51290.3 (Oryza sativa), 3'ss of exon 1
gtacgtacggtatatatatgggatccatcttcttctccaa-ttccacaatctcatc-gtttcagtctgct-tccatcac----------tcatgctactagttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
||| |||  |||| | |||    |  || |||  | |    || ||   |  ||||  |||     |||  | |||||           ||||||| ||   || | |||||||||||| | ||||| ||||| || || ||||||||||||||||||||||
gtatgta--gtatgtctatcttcttaattttcacccctgccttgcagcgtgccatccattttttcttgccatgcatcatatcatggaattcatgctgctttctcatggcagGAACTATGCTCATGACGGAGGACCGACGGCGCGCCATATGGGCCATCTATG
















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|211364013|gb|FK959502.1|FK959502
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGG
EST: gi|148973689|gb|EE024811.2|EE024811
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|91054433|gb|EB164851.1|EB164851
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|211364023|gb|FK959512.1|FK959512
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGC-ATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|74241172|gb|DT649086.1|DT649086
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|148946928|gb|EC892212.2|EC892212
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|93281436|gb|EB673700.1|EB673700
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|149008706|gb|EE040900.2|EE040900
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|211364022|gb|FK959511.1|FK959511
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|94472244|gb|EB701202.1|EB701202
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|101401215|gb|EB822286.1|EB822286
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|91877248|gb|EB407205.1|EB407205
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|148958128|gb|EC904326.2|EC904326
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTA
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTA
EST: gi|148995759|gb|EE034988.2|EE034988
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|211364027|gb|FK959516.1|FK959516
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCNATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|78104640|gb|DV523058.1|DV523058
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|76911964|gb|DV164511.1|DV164511
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|211364017|gb|FK959506.1|FK959506
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGAC
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGAC
EST: gi|76916879|gb|DV166586.1|DV166586
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|71447701|gb|DR828751.1|DR828751
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|71775307|gb|DR973185.1|DR973185
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|211364025|gb|FK959514.1|FK959514
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|50325756|gb|CO520882.1|CO520882
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|93016198|gb|EB641718.1|EB641718
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|67028270|gb|CO457019.1|CO457019
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|71444100|gb|DR825150.1|DR825150
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|149073532|gb|EE161835.2|EE161835
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
EST: gi|149075800|gb|EE164333.2|EE164333
EST:     CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCG                         GAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG
genomic: CGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG

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: 39 (upstream exon), 48 (downstream exon)
Score: 16

GCCAGGCCCCAGGACATGGACATGCCACGCAACGGGCTCAAGGAAGCCTACGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 118

GCCAGGCCCCAGGACATGGACATGCCACGCAACGGGCTCAAGGAAGCCTACGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 26

GCCAGGCCCCAGGACATGGACATGCCACGCAACGGGCTCAAGGAAGCCTACGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 171

GCCAGGCCCCAGGACATGGACATGCCACGCAACGGGCTCAAGGAAGCCTACGACCGCTGCGGCGAGATCTGTGAGGAGTATGCCAAGACGTTTTACCTCGgtacgtacgg ... ttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtacggtatatatatgggatccatcttcttctccaattccacaatctcatcgtttcagtctgcttccatcactcatgctactagttcgtcgcagGAACTATGTTGATGACAGAGGAGCGGCGCCGCGCCATATGGGCCATCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG