Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacgttcgttcataaacacctcgctcgatcgctctcatgatcatcatcatcatcatcataaggttgcatggtcgacattttcgatgtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAGCGAGAAGGGGCCACTCTTCTGACTGGAGGAAGGCCATGCGGTCCGGAAG

Basic information

species Zea mays
transcript GRMZM2G122172_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122172_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g39230.1 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------------------------gttacgttcgttcataaacacctc--gctcgatcgctctcatgatcatcatcatcatcatcataaggttgcatggtcgacattttcgatgtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAGCGAGAAGGGGCCACTCTTCTGACTGGAGGAAGGCCATGCGGTCCGGAAG
                                                                         ||| |  |  ||||   |    ||  ||  |||        ||| |   |   | |||| | ||    ||  | | |  |   | | |||| |   ||||||||||||||||||||||||||||| ||  | ||||| || || ||||||  ||||||||| ||| |||| || ||||| | ||| ||||||  | |||
gtgagtgagtctgaaattaaattccgaaaaatctgaatcatcatccatccaacgagcattttttttcttgtgagttccaataattcagtgatgattcaggcctgattaactatctgaaccagagactgatcaccgta---ctgtgttgcc--ctgctactatgttcatacagGTGGACAAGGCTCAGTATGAGAGGGTGCTCGGGTACATCGAGCAAGGCAAGGCAGAAGGGGCAACTGTTCTCACGGGAGGGAAGCCCTGCGGTAAGAAAG
















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|5005600|gb|AI711662.1|AI711662
EST:     CAGCGACCCTAGCGCCGACCAGGGCCCGCAG                         GTGG-CAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGGCCATGGCAAG
genomic: CAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
EST: gi|148942564|gb|EC887583.2|EC887583
EST:     GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAG                         GTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
genomic: GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
EST: gi|76020436|gb|DT947606.1|DT947606
EST:     GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAG                         GTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
genomic: GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
EST: gi|78083932|gb|DV512325.1|DV512325
EST:     GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAG                         GTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
genomic: GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
EST: gi|149087182|gb|EE176719.2|EE176719
EST:     GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAG                         GTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
genomic: GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
EST: gi|4835135|gb|AI670361.1|AI670361
EST:     GCGCCGACCAGGGCCCGCAG                         GTGG-CAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
genomic: GCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
EST: gi|78074898|gb|DV503332.1|DV503332
EST:     GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAG                         GTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
genomic: GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
EST: gi|148959027|gb|EC905199.2|EC905199
EST:     GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAG                         GTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
genomic: GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
EST: gi|148948769|gb|EC894170.2|EC894170
EST:     GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAG                         GTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
genomic: GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
EST: gi|78091392|gb|DV519766.1|DV519766
EST:     GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAG                         GTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
genomic: GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
EST: gi|71317747|gb|DR795632.1|DR795632
EST:     GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAG                         GTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
genomic: GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
EST: gi|148950305|gb|EC895864.2|EC895864
EST:     GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAG                         GTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
genomic: GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
EST: gi|33468129|gb|CF245178.1|CF245178
EST:     GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAG                         GTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
genomic: GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
EST: gi|148993480|gb|EE033799.2|EE033799
EST:     GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAG                         GTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
genomic: GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
EST: gi|71426117|gb|DR807167.1|DR807167
EST:     GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAG                         GTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG
genomic: GGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAG

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 3 RNA-Seq libraries.


Block sizes: 39 (upstream exon), 27 (downstream exon)
Score: 2

ACGCGTCTACGACAGGTTCGAGGAGAGGTTGGCGGAGAGGATGAGGAGCTGGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAGCGAGAAGGGGCCACTCTTCTGACTGGAGGAAGGCCATGCGGTCCGGAAG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 9

ACGCGTCTACGACAGGTTCGAGGAGAGGTTGGCGGAGAGGATGAGGAGCTGGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAGCGAGAAGGGGCCACTCTTCTGACTGGAGGAAGGCCATGCGGTCCGGAAG


Block sizes: 24 (upstream exon), 45 (downstream exon)
Score: 3

ACGCGTCTACGACAGGTTCGAGGAGAGGTTGGCGGAGAGGATGAGGAGCTGGGTCGTGGGCGACCCGTTCAGCGACCCTAGCGCCGACCAGGGCCCGCAGgttacgttcg ... gtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAGCGAGAAGGGGCCACTCTTCTGACTGGAGGAAGGCCATGCGGTCCGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcatcatcatcatcataaggttgcatggtcgacattttcgatgtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAGCGAGAAGGGGCCACTCTTCTGACTGGAGGAAGGCCATGCGGTCCGGAAG
              atcataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacgttcgttcataaacacctcgctcgatcgctctcatgatcatcatcatcatcatcataaggttgcatggtcgacattttcgatgtgcgcgcagGTGGACAAGGCTCAGTATGAGAGGGTTCTGAGCTACATTGACCATGGCAAGCGAGAAGGGGCCACTCTTCTGACTGGAGGAAGGCCATGCGGTCCGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA