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'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgataatgaagacacaatcagtgtgaagtagtcttgtgctttcggtatgttttcttagcaccttcaggctattgatctttggcattgcatacttgtcagTTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGCTTCGCACATGTGGTGGCCGGCAACCCACAGGAAGGCCTCGAGGATGCAA

Basic information

species Zea mays
transcript GRMZM2G177445_T01
intron # 9
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|116821976|gb|EC865335.1|EC865335
EST:     ATGCCTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGG                         TTCCTCGACTCAGGTGCAGTGGTGGCTCCAACTATGCTGGGACGGAGATGC
genomic: ATGCCTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGGgtacgcttac ... tacttgtcagTTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGC
EST: gi|148996261|gb|EE035541.2|EE035541
EST:     CTTTAGGTTTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGG                         TTCCTCGATTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGAGGGAGATGC
genomic: CTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGGgtacgcttac ... tacttgtcagTTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGC
EST: gi|76281722|gb|DV021290.1|DV021290
EST:     AGTGTTACTCAAGG                         TTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGC
genomic: AGTGTTACTCAAGGgtacgcttac ... tacttgtcagTTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGC
EST: gi|166675700|gb|EG172254.1|EG172254
EST:     ATGCCTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGG                         TTCCTGGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGG
genomic: ATGCCTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGGgtacgcttac ... tacttgtcagTTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGG
EST: gi|76018064|gb|DT945234.1|DT945234
EST:     ATGCCTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGG                         TTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGC
genomic: ATGCCTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGGgtacgcttac ... tacttgtcagTTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGC
EST: gi|4225549|gb|AI396002.1|AI396002
EST:     ATGCCTTTAGGTCTAAGGAATACACGCCTGCAATCGAGTGTTACTCAAGG                         TTCCTAAACTCAGGTGCAGTGGTGGCTACAACCATGCTGGGACGGAGATGC
genomic: ATGCCTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGGgtacgcttac ... tacttgtcagTTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGC
EST: gi|110533005|gb|EE037185.1|EE037185
EST:     ATGCCTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGG                         TTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGC
genomic: ATGCCTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGGgtacgcttac ... tacttgtcagTTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGC
EST: gi|211523270|gb|FL465591.1|FL465591
EST:     ATGCCTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGG                         TTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGC
genomic: ATGCCTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGGgtacgcttac ... tacttgtcagTTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGC

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), 47 (downstream exon)
Score: 88

ATGGAATGGTGATATATCTGAGAGCTTTGTTGTTAAGAGGCGTGCAGACAATGCCTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGGgtacgcttac ... tacttgtcagTTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGCTTCGCACATGTGGTGGCCGGCAACCCACAGGAAGGCCTCGAGGATGCAA


Block sizes: 37 (upstream exon), 47 (downstream exon)
Score: 7

ATGGAATGGTGATATATCTGAGAGCTTTGTTGTTAAGAGGCGTGCAGACAATGCCTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGGgtacgcttac ... tacttgtcagTTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGCTTCGCACATGTGGTGGCCGGCAACCCACAGGAAGGCCTCGAGGATGCAA


Block sizes: 46 (upstream exon), 32 (downstream exon)
Score: 13

ATGGAATGGTGATATATCTGAGAGCTTTGTTGTTAAGAGGCGTGCAGACAATGCCTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGGgtacgcttac ... tacttgtcagTTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGCTTCGCACATGTGGTGGCCGGCAACCCACAGGAAGGCCTCGAGGATGCAA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 25

ATGGAATGGTGATATATCTGAGAGCTTTGTTGTTAAGAGGCGTGCAGACAATGCCTTTAGGTCTAAGGAATACACGACTGCAATCGAGTGTTACTCAAGGgtacgcttac ... tacttgtcagTTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGCTTCGCACATGTGGTGGCCGGCAACCCACAGGAAGGCCTCGAGGATGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgttttcttagcaccttcaggctattgatctttggcattgcatacttgtcagTTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGCTTCGCACATGTGGTGGCCGGCAACCCACAGGAAGGCCTCGAGGATGCAA
                         tattgat  putative branch site (score: 25)
     ttttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgataatgaagacacaatcagtgtgaagtagtcttgtgctttcggtatgttttcttagcaccttcaggctattgatctttggcattgcatacttgtcagTTCCTCGACTCAGGTGCAGTGGTGGCTCCAACCATGCTGGGACGGAGATGCTTCGCACATGTGGTGGCCGGCAACCCACAGGAAGGCCTCGAGGATGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - -gacacaa
- - - - - - - - - - - - - - - - - - -tgctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattgca