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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGACCGTGTTTAAGGAAACATACAGCAAGCTCAAGGAGGAGATGCTAGACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctctcttcgcctccaggctccagccctccactcagtttagtttactgtgatctctctggcggtcccgtcagctctttcgatttctaccgagttt...

Basic information

species Zea mays
transcript GRMZM2G147721_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 1
CAAGACCGTGTTTAAGGAAACATACAGCAAGCTCAAGGAGGAGATGCTAGACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctctcttcgcctccaggctccagccctccactcagtttagtttactgtgatctctctggcggtcccgtcagctctttcgatttctaccgagttt-
|||| ||| |||   ||| | |||||||| |||||||||||||||||| || ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||  |  | |||      |      |  ||    |   || | | |     |||   |  ||       |         | |||  
CAAGGCCGCGTTCGCGGAGATATACAGCAGGCTCAAGGAGGAGATGCTCGAGGACCCGGCCTTCGAGTTCACCGACGAGTCGCTCCAGTGGATCGACCGCgtaatgctctcttccccgtctcgatcctttatgctgggagggata-cggatgttggtttttgatctggtttagcgagaggggagggagggggtggcgttga
















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|211272079|gb|FL317340.1|FL317340
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|148972761|gb|EE023734.2|EE023734
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|149102315|gb|EE188183.2|EE188183
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|149081093|gb|EE170194.2|EE170194
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|211528502|gb|FL328860.1|FL328860
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|148986685|gb|EE030467.2|EE030467
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|211537181|gb|FL316595.1|FL316595
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|71437045|gb|DR818095.1|DR818095
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|211162026|gb|FL334313.1|FL334313
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGT-CAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|211507953|gb|FL346110.1|FL346110
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|211302622|gb|FL366315.1|FL366315
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|211278408|gb|FL366607.1|FL366607
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|18659682|gb|BM500468.1|BM500468
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGNTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|211268113|gb|FL358780.1|FL358780
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|211222998|gb|FL350874.1|FL350874
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|211226829|gb|FL341085.1|FL341085
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|148942982|gb|EC888030.2|EC888030
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|211056216|gb|FL359449.1|FL359449
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|148943253|gb|EC888314.2|EC888314
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|74235474|gb|DT643388.1|DT643388
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|211274552|gb|FL349465.1|FL349465
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|211460036|gb|FL333652.1|FL333652
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|211049850|gb|FL341779.1|FL341779
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
EST: gi|211322449|gb|FL341510.1|FL341510
EST:     ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGC                         ATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC
genomic: ACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTC

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: 44 (upstream exon), 49 (downstream exon)
Score: 52

CAAGACCGTGTTTAAGGAAACATACAGCAAGCTCAAGGAGGAGATGCTAGACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTCATTGATAGCTACAGGATATTGAAGGGTGTTGATGTTCTGAGCAAGGAGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 89

CAAGACCGTGTTTAAGGAAACATACAGCAAGCTCAAGGAGGAGATGCTAGACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTCATTGATAGCTACAGGATATTGAAGGGTGTTGATGTTCTGAGCAAGGAGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 36

CAAGACCGTGTTTAAGGAAACATACAGCAAGCTCAAGGAGGAGATGCTAGACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTCATTGATAGCTACAGGATATTGAAGGGTGTTGATGTTCTGAGCAAGGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

CAAGACCGTGTTTAAGGAAACATACAGCAAGCTCAAGGAGGAGATGCTAGACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctct ... tctggagcagATGTTGGACTACAATGTGCTCGGAGGAAAGTGCAATCGCGGGCTCTCTGTCATTGATAGCTACAGGATATTGAAGGGTGTTGATGTTCTGAGCAAGGAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGACCGTGTTTAAGGAAACATACAGCAAGCTCAAGGAGGAGATGCTAGACGACCCCGCCTTCGAGTTCACCGACGAGTCGCTACAGTGGATCGACCGCgtaatgctctcttcgcctccaggctccagccctccactcagtttagtttactgtgatctctctggcggtcccgtcagctctttcgatttctaccgagttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctccac