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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcacaaccaattttctgcttgcttctcttcccttaggtttacatcatgctgatattccataacaatttcagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGACGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA

Basic information

species Zea mays
transcript GRMZM2G141587_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 5
gtatgcacaaccaattttctgcttgcttctcttcccttaggtttacatcatgctgatatt-ccataacaatttcagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGACGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
||||||    |||  |    |||| ||||| ||    |    |  |||| |||| ||||   |||  | ||||||||||| ||  ||||||||||  |||| || |||||||| |||||||||||||||||||||||||| ||||||||||| || || || ||||| ||||||||
gtatgctttcccacctcatcgcttacttctgtt----tgatataccatcttgctaatataatcatccccatttcagTTCGGTCATCTAAATTTATCACACGGAAACAATGGGTAGTTGCTGGTGCCGACGATATGTTCATACGTGTGTACAATTACAATACGATGGATAAGGTCAA

upper sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 5
--------------------------------------gtatgcacaaccaattttctgcttg---cttctcttcccttaggtttacatcatg---ctgatattccataacaattt-cagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGACGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                       | |||      | |  | ||||||       | ||    |  || ||  |||||   || |||| |   |  | ||| ||||| | || || || ||||||||||| || || ||||||||||| || || || |||||||| || ||||| || || || ||||||||||| || || ||
gtgggtgaacgttttatagtctatttcattggttgtgtatctgccttttgattcatttgcttgaagtcattttttttctttgtatatttcatgggtctcatatacagcatgattttgcagTTAGGTCAGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCAGGGGCAGATGATATGTTTATTCGTGTATATAATTACAACACAATGGATAAAGTTAA

upper sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------gtatgcacaaccaattttctgcttgcttc-----tcttcccttaggtttacatc-atgctgatattccataacaattt-cagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGACGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                                              |  || | |  |  || | ||  |  |||     |  |  |||||     ||   | |||  ||| | | |  | ||| ||||| | ||||| || ||||||||||| || || |||||||||||||| || || |||||||| || ||||| || || || ||||||||||| || |||||
gtacatgaagtcatgaaccttttctggtccatttgtttgtctatatatctcttgatgcatttgcttgaagacacttttctttgtatatttcatgatttcttacttagaagaccactgaagctcttatacaacatgattttgcagTTAGATCGGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCTGGAGCAGATGATATGTTTATTCGTGTATATAATTACAACACAATGGATAAAGTCAA

upper sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 5
--------------------------------------gtatgcacaaccaattttctgcttgct-----tctcttcccttaggt-ttacatcatg-ctgatattccataacaattt-cagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGACGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                       | |||      | |  | |||||| |     | |||| | |||  | || |||   | || |||| |   |  | ||| ||||| | || || || ||||||||||| || || ||||||||||| || || || |||||||| || ||||| || || || ||||||||||| || || ||
gtgggtggacgttttttagtctatttcattgatcgtatatctgcctcttgattcatttgcttgatgtcattttctttctttatatatttcatggggtctcatatgcagcatgattttgcagTTAGGTCAGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCAGGGGCAGATGATATGTTTATTCGTGTATATAATTACAACACAATGGATAAAGTTAA

upper sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------gtatgcacaaccaattttct--gcttgcttc-----tcttcccttag--gtttaca-------tcatgctgatattccataacaattt-cagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGACGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                                              |  || | |  || ||||||  |  |  |||     |  |  |||||  | | ||        | || |   ||| | | |  | ||| ||||| | ||||| || ||||||||||| || || |||||||||||||| || || |||||||| |||||||| || || || ||||||||||| || |||||
gtacttgaagacgtgaaccttttttggtccatttgtttgtatatctacctcttgatgcatttgcttgaagacacacttttctttgtatatttcatgatttcttacttagaagatcactggagctcttatacaagtatacaacatgattttgcagTTAGATCGGCCAAGTTTATTGCACGCAAACAGTGGGTTGTTGCTGGAGCAGATGATATGTTTATCCGTGTATATAATTACAACACAATGGATAAAGTCAA

upper sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------gtat-gcacaaccaattttc-----tgcttgcttctcttcccttaggtttacatcatgctgatattccata--acaattt--cagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGACGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                  ||| |  |||    || |      | ||   | ||| |  ||    | |   | || ||| | ||  |||  |  | ||  ||||||| || || || ||| | ||||| |||||||||||||| || || || || |||||||  |||||||| ||||| || ||||| ||||||||||| ||
gtatacggcttttgttcttttgtgtcttttgttatattgttcaagtttttgttgtatgtactaagtactcgtgtctagtttgttacttattctgcttttttatattatgactttgcagTTCGGTCAGCCAAGTTTGTAGCACGAAAGCAATGGGTTGTCGCAGGAGCTGATGATATGTATATCCGTGTATACAATTACAACACCATGGACAAGGTTAA

upper sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------gtatgcacaaccaattttctgcttgct-tctcttcccttaggtt-tacatca----tgctgatattc-cataacaattt-cagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGACGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                              |       |   |||||   |||||| | | || ||||   |  |   ||     | |||| |||   |||  | ||| ||||| | ||||| || |||||| | || |||||||||||||| ||||| || || ||||||| ||||||||| ||||| || || |||||||||||||||||
gtataacaagtttatgagcatcttctgatttcattgttatagatttttcacttgctgtatattgccttgtatagtctgtcgctgttactgaaatttatatatgactttgcagTTAGGTCGGCCAAGTTTATTCCGCGCAAGCAATGGGTTGTGGCTGGAGCGGATGATATGTACATCCGTGTATACAATTACAATACAATGGACAAGGTCAA

upper sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------------------gtatgcacaaccaattttctgcttgcttctcttcccttag---gtttacatcatgct--gatattccataacaatttcagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGACGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                                    |   |   | | |||||        ||||||    || |   | |||   |||| |   || || ||| |  ||| ||||| | || || || ||||| ||||| |||||||||||||||||||| || || |||||||| || ||||| ||||| |||||||||||||| ||||| ||
gtatgtacatgtactttatctgtttccatatgctctatttggtgtgattgaattcccttgatccatttttactcaatttctctcttattggtaaggttattacatgtttcaattttacattatcattgcagTTAGGTCAGCGAAGTTTATAGCACGCAAGCAATGGGTTGTTGCTGGAGCTGATGATATGTTTATTCGTGTATACAATTATAACACAATGGATAAGGTTAA

upper sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------------------------gtatgcacaaccaattttctgcttgcttctcttcccttaggtttacatcatgctgatattccataacaatttc---agTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGACGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                                                                                         | ||   | |   | |     |||   |  |  | | |   |      | |     ||  | |     ||||   ||| || || || || |||||  | |||||||| |||||||| ||| |  | || || ||||||||||| ||||| ||||||||||| |||||||| || ||
gtacgttgtttgagaccatgtttatccgtccgttccatggttcagctgtcattgtagtagtcactcgcgagttttattacagtcgtcactcacagtgcatctttctgtgtttagctgttctctattttgaaaccatcacttgaaagtgctgagaggagttcatctcgttctgttttctgcagTGCGATCAGCGAAGTTTATCCCCCGTAAGCAGTGGGTTGTGGCTTGCTCTGATGACATGTTCATCCGAGTGTATAACTATAACACGATGGACAAAGTGAA

upper sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ09529 (Selaginella moellendorffii), 3'ss of exon 2
-----------------------------------gtatgcacaaccaattttctgct--tgcttctc---ttcccttaggtttacatcatgctgatattccataac--aatttcagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGACGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                   |  |      |||| | | || |  | | ||||   ||  || || ||  |   |  |   | |   ||  |    ||  ||| || ||||| || || ||  | || ||||| ||| | || |||||||||||||| |||| ||| || || |||||||| || || ||||||||||||||
gtaacttttggagtggatttctctaagtccctcgagagtatttttccaagtctgtgttgctccatctcgatttttctaagtttctctctaaaccattgtgtgatctcttgcttgtagTCCGCTCGGCCAAGTTCATATCGCGAAAGCAGTGGATAGTCGCTGGTGCCGACGACATGTACATTCGAGTCTACAACTACAATACCATGGACAAGGTCAA

upper sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ36319 (Selaginella moellendorffii), 3'ss of exon 2
-----------------------------------gtatgcacaaccaattttctgct--tgcttctc--ttcccttaggtttacatc---atgctgatattccataacaatttcagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGACGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                   |  |      |||| | | || |  | | ||||  ||    || ||||   ||   |   |  | |    |     ||  ||| || ||||| || || ||  | || ||||| ||| | || |||||||||||||| |||| ||| || || |||||||| || || ||||||||||||||
gtaacttttggagtaaatttctctaagtcccttgagagtatttttccaagtctgtgttgctccatctcgatttttctaagtttctctctaaaaaattgtgtgatctcttgcttgtagTCCGCTCGGCCAAGTTCATATCGCGAAAGCAGTGGATAGTCGCTGGTGCCGACGACATGTACATTCGAGTCTACAACTACAATACCATGGACAAGGTCAA

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|76282808|gb|DV022376.1|DV022376
EST:     ACAATGGTGAAATCATTTGAAGTCACGGATTTACCAG                         TTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCG
genomic: ACAATGGTGAAATCATTTGAAGTCACGGATTTACCAGgtatgcacaa ... acaatttcagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCG
EST: gi|78078423|gb|DV506837.1|DV506837
EST:     ACAATGGTGAAATCATTTGAAGTCACGGATTTACCAG                         TTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCG
genomic: ACAATGGTGAAATCATTTGAAGTCACGGATTTACCAGgtatgcacaa ... acaatttcagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgcttctcttcccttaggtttacatcatgctgatattccataacaatttcagTTCGTTCGGCTAAATTTATTGCACGTAAGCAATGGGTTGTTGCTGGTGCCGACGATATGTTCATCCGTGTGTACAACTATAACACAATGGACAAGGTCAA
                                        ccataac  putative branch site (score: 3)
                                          ataacaattt  TA-rich tract