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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcctctcaaagttgtttgttgtgctgaatattccatcgcaattttcaacaaaactcccgaatcatatgtaagaggtctgtttcccagatttgttgtgctgaaccctttctttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG

Basic information

species Zea mays
transcript GRMZM2G019986_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019986_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 6
------gtaagtgcctctcaaagttgtttgt------tgtgctga--atattccatcgcaattttcaacaaaactcccgaatcatatgtaagaggtctgtttcccagatttgttgtgctgaaccctttctttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG
        |||| | | |     |  |||||      | | |  |    ||| || |  ||  | |||||  |  ||| | |||   ||||   || |  |    || ||||    |||||||  |||||| |||||||||||||||||||||||||||| |||||||| || ||||| ||||| ||||||||||||||||||||||| | |
gtaagatcaagtacttttttttttcatttgtgttaactattccaatggaatttcaacaaaagatccaacaggatcccccattcactagtaat--gtttaataggtaggtttgaacagctgaacattttctt-ggcagGTGACATTTTTCCAACAAGGCACCCTTCCATGTGTTTCTGCTGATGGCAGATTTATTATGGAGACACCATACAAG

upper sequence: GRMZM2G019986_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 6
gtaagtgcctctcaaagttgtttgttgtgctgaatattccatcgcaattttcaacaaaactcccgaatcatatgtaagaggtctgtt-tcccagatttgttgtgctgaaccctttctttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG
                                         |   |  | | ||      ||  | |  ||  |||   | | |  | |     | ||    ||      ||| | |     |||| || |||||||| ||||| ||| | || || || ||    ||||||||||||||||||||||| ||||| |||
----------------------------------------gtaagatgtctaaatctttttcatgtactattagtactcgttttactattgtttacttaccatggactcacctctttgatatagGTTACCTTTTTCCAGCAAGGAACAATCCCTTGTGTTTCCAAGGATGGTAGATTTATTATGGAGACTCCATACAGG
















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|71774724|gb|DR972602.1|DR972602
EST:     CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCAA                         GTGACATTTTTCCAACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGA
genomic: CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCAAgtaagtgcct ... tctttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGA
EST: gi|149014076|gb|EE043603.2|EE043603
EST:     CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCAA                         GTGACATTTTTCCCACAAGGCACACTTCCCTGCGTCTCTGCCGATGGTAGA
genomic: CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCAAgtaagtgcct ... tctttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGA
EST: gi|78089272|gb|DV517646.1|DV517646
EST:     CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCAA                         GTGACATTTTTCCAANCA-GGCACACTTCCATGCGTCTCTGCCGATGGTA
genomic: CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCAAgtaagtgcct ... tctttggcagGTGACATTTTTCCAA-CAAGGCACACTTCCATGCGTCTCTGCCGATGGTA
EST: gi|148951106|gb|EC896776.2|EC896776
EST:     CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCAA                         GTGACATTTTTCCAACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGA
genomic: CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCAAgtaagtgcct ... tctttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGA
EST: gi|148991365|gb|EE032856.2|EE032856
EST:     CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCCA                         GTGACATTTTTCCAACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGA
genomic: CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCAAgtaagtgcct ... tctttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGA
EST: gi|78112754|gb|DV531148.1|DV531148
EST:     CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCAA                         GTGACATTTTTCCCACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGA
genomic: CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCAAgtaagtgcct ... tctttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGA
EST: gi|148935256|gb|EC879293.2|EC879293
EST:     CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCAA                         GTGACATTTTTTCCAACA-GGCACACTTCCATGCGTCTCTGC
genomic: CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCAAgtaagtgcct ... tctttggcagGTGACATTTTT-CCAACAAGGCACACTTCCATGCGTCTCTGC
EST: gi|149102322|gb|EE188185.2|EE188185
EST:     CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCAA                         GTGACATTTTTCCAACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGA
genomic: CTCGCAAATTCTTCGAAACCCGTAGATACTTTGGCCTAGACCCTGACCAAgtaagtgcct ... tctttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgtaagaggtctgtttcccagatttgttgtgctgaaccctttctttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG
                                        ccctttcttt  CT-rich tract
                         atttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcctctcaaagttgtttgttgtgctgaatattccatcgcaattttcaacaaaactcccgaatcatatgtaagaggtctgtttcccagatttgttgtgctgaaccctttctttggcagGTGACATTTTTCCAACAAGGCACACTTCCATGCGTCTCTGCCGATGGTAGATTTATTATGGAGACACCATATAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA