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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcttttatctcccaacgttcgcctctccccgaattatcttgttgcggcggccgtgcctccgctctgtcgttgtccggtcgcccggtgctttgattgaatcgactcggccgattgattccaatttccatccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCCCCGCTGGACGACGAGGCCGGCATCGCCGTCATCGCGCACGCTTTCAGCC

Basic information

species Zea mays
transcript GRMZM2G024315_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024315_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g43090.1 (Oryza sativa), 3'ss of exon 1
gtctcttttatctcccaacgttcgcctctccccgaattatcttgttgcggcggccgtgcctccgctctgtcgttgtccggtcgcccggtg-ctttgattgaatcgactcggccgat--tgattccaatttccatccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCCCCGCTGGACGACGAGGCCGGCATCGCCGTCATCGCGCACGCTTTCAGCC
      |  |  | ||  || | ||     |   ||||  | |  | |  ||    | | | || || ||    |     ||| || ||| |  ||| ||    || |||   |||  ||| | | |   || | | ||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||| |||||||| ||||||  |||||||||||||||||| ||| |||
-----gtgaacatgcc--cgcttgctcgatcgtcaatt--cctacttccccgtatttccgttcgttcggtttgcgctgaatcggccagtgacagtgagtg---tgaatcgatggatgttgaattcgacgaccttgc-tgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTCACGGGCGCGTACAACTCGCCGCTCGACGACGACGCCGGCGCCGCCGTCATCGCGCACGCCTTCCGCC
















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:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|211043713|gb|FL336928.1|FL336928
EST:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTG
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTG
EST: gi|211083193|gb|FL315299.1|FL315299
EST:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|76014741|gb|DT941911.1|DT941911
EST:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|8367347|gb|BE050292.1|BE050292
EST:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|148966879|gb|EE017999.2|EE017999
EST:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|149109975|gb|EE293785.2|EE293785
EST:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|211115050|gb|FL357310.1|FL357310
EST:     AAGCACGTCCGG-T--TCCCCGCGTCAAGCTCGGCACCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCATACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|76934797|gb|DV174022.1|DV174022
EST:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|71438898|gb|DR819948.1|DR819948
EST:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|211043426|gb|FL323571.1|FL323571
EST:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|71430218|gb|DR811268.1|DR811268
EST:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|19822526|gb|BQ048550.1|BQ048550
EST:     AAGCACGTCCGGTTCCT-CCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         G-GTCCAAGCTGGGGTTCGGG-GCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|71438372|gb|DR819422.1|DR819422
EST:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|211312220|gb|FL336750.1|FL336750
EST:     AAGCACGTCCGG-T--TCCCCGCGTCAAGCTCGGCACCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCATACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|211482867|gb|FL313329.1|FL313329
EST:     AAGCACGTCCGG-T--TCCCCGCGTCAAGCTCGGCACCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCATACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|71327903|gb|DR800586.1|DR800586
EST:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|149014830|gb|EE044532.2|EE044532
EST:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|148931634|gb|EC874774.2|EC874774
EST:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|211525034|gb|FL310989.1|FL310989
EST:     AAGCACGTCCGG-T--TCCCCGCGTCAAGCTCGGCACCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCATACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|13125896|gb|BG316571.1|BG316571
EST:     TCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: TCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
EST: gi|78090111|gb|DV518485.1|DV518485
EST:     AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAG                         GTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC
genomic: AAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCC

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), 49 (downstream exon)
Score: 39

GTTCGCAGTTCAGTTCACACTTCACAGGCGAGCAGCGACCATGGATACCCAAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCCCCGCTGGACGACGAGGCCGGCATCGCCGTCATCGCGCACGCTTTCAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 339

GTTCGCAGTTCAGTTCACACTTCACAGGCGAGCAGCGACCATGGATACCCAAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCCCCGCTGGACGACGAGGCCGGCATCGCCGTCATCGCGCACGCTTTCAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 367

GTTCGCAGTTCAGTTCACACTTCACAGGCGAGCAGCGACCATGGATACCCAAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCCCCGCTGGACGACGAGGCCGGCATCGCCGTCATCGCGCACGCTTTCAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

GTTCGCAGTTCAGTTCACACTTCACAGGCGAGCAGCGACCATGGATACCCAAGCACGTCCGGTTCCTCCCCGCGTCAAGCTCGGCATCCAGGGATTCGAGgtctctttta ... atccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCCCCGCTGGACGACGAGGCCGGCATCGCCGTCATCGCGCACGCTTTCAGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccggtgctttgattgaatcgactcggccgattgattccaatttccatccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCCCCGCTGGACGACGAGGCCGGCATCGCCGTCATCGCGCACGCTTTCAGCC
                            gattgat  putative branch site (score: 83)
                                        tttccatcc  putative PPT
       tttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcttttatctcccaacgttcgcctctccccgaattatcttgttgcggcggccgtgcctccgctctgtcgttgtccggtcgcccggtgctttgattgaatcgactcggccgattgattccaatttccatccatgtagGTGTCCAAGCTGGGGTTCGGGTGCATGGGGCTGACGGGCGCGTACAACTCCCCGCTGGACGACGAGGCCGGCATCGCCGTCATCGCGCACGCTTTCAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA