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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGCGCCTGCTGCGAGGCCAGCCTGCGCCGCCTCGGCATCGACTGCATCGACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggagcctgcctgcacattcggtctgccttaaagcagtcggcgttgttggtgtgtttgctcatgtgaaatctttgttcgaaattatcgcag

Basic information

species Zea mays
transcript GRMZM2G024315_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024315_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g43090.1 (Oryza sativa), 5'ss of exon 3
TCGCGCCTGCTGCGAGGCCAGCCTGCGCCGCCTCGGCATCGACTGCATCGACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggagcctgcctgcacattcggtc--tgccttaaagcagtcggcgttgttggtgtgtttgc-tcatgtgaaatctttgttcgaaattatcgcag------------
 |||||||||||||||||||||||  ||||||||||| |||||| ||||||||||||||||||||||||| | |||||||| |  ||||||||||| ||||||||| |  ||  |  || |  |   |   |  |||    ||||         |          |  | ||| || ||||   | |  |||   |  |            
GCGCGCCTGCTGCGAGGCCAGCCTCGGCCGCCTCGGCGTCGACTACATCGACCTCTACTACCAGCACCGCGTCGACACCACCATCCCCATCGAGGACACGgtctcttgctccacctcgccccctttcttgatttctttcttcagttctttacccttcctcacacacaccttgtaaattcttgtattgccattcgggttggtgctgaactag
















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|71773863|gb|DR971754.1|DR971754
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|91878930|gb|EB408887.1|EB408887
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|76014741|gb|DT941911.1|DT941911
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|148966879|gb|EE017999.2|EE017999
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|149109975|gb|EE293785.2|EE293785
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCTGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|18450430|gb|BM428708.1|BM428708
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAG
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAG
EST: gi|71438898|gb|DR819948.1|DR819948
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|60399433|gb|DN232245.1|DN232245
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|211043426|gb|FL323571.1|FL323571
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|71430218|gb|DR811268.1|DR811268
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|19822526|gb|BQ048550.1|BQ048550
EST:     ACCTCTACTACCAGCACCGCATGGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGNGGAGGAGGGTAAGGNCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|71438372|gb|DR819422.1|DR819422
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|211312220|gb|FL336750.1|FL336750
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAATTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|211482867|gb|FL313329.1|FL313329
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAATTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|71327903|gb|DR800586.1|DR800586
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|149014830|gb|EE044532.2|EE044532
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|148931634|gb|EC874774.2|EC874774
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|211525034|gb|FL310989.1|FL310989
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAATTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAA
EST: gi|14204195|gb|BG837872.1|BG837872
EST:     CCTCTACTACCCAGCACCGCATTGACACCACAATTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: CCTCTACTA-CCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
EST: gi|78090111|gb|DV518485.1|DV518485
EST:     ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACG                         ATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA
genomic: ACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGA

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), 48 (downstream exon)
Score: 36

TCGCGCCTGCTGCGAGGCCAGCCTGCGCCGCCTCGGCATCGACTGCATCGACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGATTGTCAGAGGCGAGCCCGGACACCATCAGGCGTGCACATGCTGTGCACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 337

TCGCGCCTGCTGCGAGGCCAGCCTGCGCCGCCTCGGCATCGACTGCATCGACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGATTGTCAGAGGCGAGCCCGGACACCATCAGGCGTGCACATGCTGTGCACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 342

TCGCGCCTGCTGCGAGGCCAGCCTGCGCCGCCTCGGCATCGACTGCATCGACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGATTGTCAGAGGCGAGCCCGGACACCATCAGGCGTGCACATGCTGTGCACC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 115

TCGCGCCTGCTGCGAGGCCAGCCTGCGCCGCCTCGGCATCGACTGCATCGACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggag ... attatcgcagATTGGCGAGCTCAAGAAGCTGGTGGAGGAGGGTAAGGTCAAGTACATCGGATTGTCAGAGGCGAGCCCGGACACCATCAGGCGTGCACATGCTGTGCACC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGCGCCTGCTGCGAGGCCAGCCTGCGCCGCCTCGGCATCGACTGCATCGACCTCTACTACCAGCACCGCATTGACACCACAACTCCCATCGAGGAGACGgtctctggagcctgcctgcacattcggtctgccttaaagcagtcggcgttgttggtgtgtttgctcatgtgaaatctttgttcgaaattatcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA