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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattacatacctccacacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgccataaaatgaaacatgatatgaccttcctccaaaaaatgttctaatgcctgatgctcctgatgctttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT

Basic information

species Zea mays
transcript GRMZM2G100560_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100560_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g36710.1 (Oryza sativa), 3'ss of exon 5
----------------gtattacatacctccacacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgccataaaatgaaacatgatatgaccttcctccaa------aaaatgttctaatgcct-gatgctcctgatgctttt------------tccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT
                | ||||    | |||| | ||      |   ||  ||   || | ||||||   | | |||  | |   |    | |   ||||| ||  | |    |    ||||      |||||  || | ||  | ||||   |  ||  || |             |  | ||||||||||||||  | ||||| |||||||| ||||||||||||||||||||||||||| | ||||||||||||||||| ||||||||||||||||| ||||||||
gtatttccccccaaaagaattatgcccttccaaagaacttgtgtttcatcttatgttttttttttac---tctattatgaatttgtcctgacatggtgaaa-atactgttttttgaaaccaaatagtgaaaatactcaagtgttttgatgacacacatatttatgattggtcaatgccttcttttacagATGAAAGATTAAATGATATTGTTGGTAGTGCATACTATGTTGCTCCAGAAGTCCTACATAGGTCATATAGCACGGAAGCAGACATGTGGAGTATTGGTGT

upper sequence: GRMZM2G100560_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G02340.1 (Glycine max), 3'ss of exon 6
gtattacatacctccacacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgccataaaatgaaacat-gatatgaccttcctccaaaaaatgttctaatgcctgatgctcctgatgctttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT
                                                    | | ||||  | || |     |||||    | |||| | |  ||  ||  |  | | || ||  |    | | ||  | |   |  | | |     |||||||||||| | || ||||||||||| || |||||||| |||||||| || || ||| | || |||||||||||    |||||||| || ||||| ||||||||
---------------------------------------------------tagtctgttccatgtac----tcataacccaagacattgttgggatatttatggatataaggtcatccctcttaatttttcccttcgtgtgtgttgatttacagATGAACGACTGAATGACATTGTCGGGAGTGCATATTATGTTGCACCTGAGGTCCTTCACAGGTCATATAGTCTGGAAGCAGATATATGGAGTATTGGTGT

upper sequence: GRMZM2G100560_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G05750.1 (Glycine max), 3'ss of exon 5
gtattacatacctccacacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgccataaaatgaaacat-gatatgaccttcctccaaaaaatgttctaatgcctgatgctcctgatgctttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT
                                                    | | ||||  | || |     |||||    | |||| | |  ||  ||  |  | | || |   |    | | ||  | |   |  | | |     |||||||||||  | || |||||||||||||| ||||| || |||||||| || || ||| | || |||||||||||    |||||||| || ||||| ||||||||
---------------------------------------------------tagtctgttccatgtac----tcataacccaagacattgttgggatatttatggatataaggccatccctcttaatttttcccttcatgtgtgttgatttacagATGAGCGACTGAATGACATTGTTGGGAGTGCGTATTATGTTGCACCTGAGGTCCTTCACAGGTCATATAGTCTGGAAGCAGATATATGGAGTATTGGTGT

upper sequence: GRMZM2G100560_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G49370.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattacatacctccacacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgccataaaatgaaacatgatatgaccttcctccaaaaaatgttctaatgcctgatgctcctgatgctttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT
                                  ||||   | ||||   |   | |  || | | |  |     ||  ||   || | | | |||         ||  |||    ||||  |  |  |  |  |  | ||   |  |    |||| |  | || || ||  | || |||||||||||||||||||| || |||||  | || || || |||||||| |||||||| || ||||| ||||||||
----------------------------------gtaattctttgttcctctt-tcttatacatgactctgcttgtagtattttac-ttagaagact--------aaggatg---gaatgttttttttttttttta-tgttgggctttaactagATCAGCGTCTCAACGATGTGGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTTCACAGATCCTATAGCACCGAAGCAGATATATGGAGCATTGGTGT

upper sequence: GRMZM2G100560_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G24430.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattacatacctccacacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgccataaaatgaaacatgatatgaccttcctccaaaaaatgttctaatgcctgatgctcctgatgctttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT
                                                   ||  || |  |   ||| ||| |||   || |  | ||  |  | ||   |   | || | |||   |  |   |  |  |  |   | ||     | | ||||| |  | || |||||  |||| |||||||||||||||||||| || |||||  | |||||||| || ||||| |||||||| |||||||| || |||||
-------------------------------------------------gtaaccatatatgt--tcccttggcatt--attagtcttgcca-aatctcatttgtacaagttttccgctcacatttcttatttgttaatcttttatatatgcagATCAGCGTCTCAATGATGTTGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTCCATAGGTCTTACAGCACTGAAGCAGATATGTGGAGCATCGGTGT

upper sequence: GRMZM2G100560_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G46700.2 (Arabidopsis thaliana), 3'ss of exon 4
gtattacatacctccacacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtc-cattgccataaaatgaaacatgatatgaccttcctccaaaaaatgttctaatgcctgatgctcctgatgctttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT
                                                         || |||  |  ||||     |        ||  |||   | |||||   |      | ||| ||           ||||  |   | || |  | |||||||||| || ||||| || ||||||||||| |||||||| || || ||||| || || ||||||||||||   || || || || ||||| ||||| ||
---------------------------------------------------------gtaagacttttcattctttcaggccttgtcactata---ctttccttatagctgcctactagtg------aaatttgat--tgaattcctcaatgcagATGAAAGACTGAATGATATAGTTGGAAGTGCCTACTATGTCGCGCCTGAAGTTTTACACAGGTCATATAGCCTTGAGGCTGATATATGGAGTATTGGAGT

upper sequence: GRMZM2G100560_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 5
gtattacatacctccacacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgcca-taaaatgaaacatgatatgaccttcctccaaaaaatgttctaatgcctga-tgctcctgatgctttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT
                                                        ||||  || ||| | | || | |  |    |    | |  | |   | ||   | |  ||| | |  ||| ||   | |     | ||      ||  |||| || | || ||||| |||||||||||||||||||||||||| || |||||  | || || || || |     ||||| ||  | ||||| ||||| ||
--------------------------------------------------------tgtttcaactccttagacaatcacctctctctctctctctcgtgtttgcactgattcatcttaagtttgaatgtaacagtcagctcttttatgcttgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT

upper sequence: GRMZM2G100560_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv15s0048g02840.t01 (Vitis vinifera), 3'ss of exon 5
gtattacatacctccacacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgccataaaatgaaacatgatatgaccttcctccaaaaaatgttctaatgcctgatgctcctgatgctttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT
                                             ||| | || |  | | |    | ||| || |   |  |  ||  ||   |  || ||        |||| |    |||     |||  ||      | |   | | |||||||||| || ||||| |||||||||||||||||||||||||| || |||||  | ||||| || |||      |||||||| || |||||  |||| ||
------------------------------------------tcatttcataacttagcttgttacctatttccctctca--agtcaaaatggaaattttcttacccgtttgtttttccccct-----tccaaata-----tgcatatatgcagATGAAAGACTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCTGAAGTTCTCCATAGATCCTATTATCTGGAAGCAGATATTTGGAGTGTTGGCGT

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|211246069|gb|FL212418.1|FL212418
EST:     TTCTCCTATGAAGATAATTGATTTTGGTCTCTCAGATTTTATAAGACCAG                         ATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAG
genomic: TTCTCCTATGAAGATAATTGATTTTGGTCTCTCAGATTTTATAAGACCAGgtattacata ... ccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctccaaaaaatgttctaatgcctgatgctcctgatgctttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT
                            ctcctgatgctttttc  CT-rich tract
     aaaaaatgttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattacatacctccacacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgccataaaatgaaacatgatatgaccttcctccaaaaaatgttctaatgcctgatgctcctgatgctttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA