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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaaataaatgatgttttcagatgaatacaatgtttttgatgccttctaatctaattaaaagatggttgagctttatgattgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA

Basic information

species Zea mays
transcript GRMZM2G012501_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012501_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 4
gttaaataaatgatgttttcagatgaatacaatgtttttgatgccttctaatctaattaaaagatggttgagctttatgattgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA
|| |||  ||   |||||| ||||  ||  | | |   |  |  ||| || | | |||  ||  || ||||  ||||       || |||| |||||||||||||||||||| ||||| || ||||| |||||||| ||||||||||||||||||||||| |||||||| ||||||||||||||||| |
gtcaaaggaa-actgtttttagatccatgaattataacttgtttcttgtattgtcattctaaattgtttgaattttaca----caacagGTTATCATAGTCACAAGCTCATTAATGAAAGATATGAACAGCAAGACGGATATGTACCGTGCCAATGCTATCAGAGTTCTGTGTAGAATAATTGATGGCA

upper sequence: GRMZM2G012501_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G12610.2 (Glycine max), 3'ss of exon 4
gttaaataaa-tgatgttt--tcagat----gaatacaatgtttttgatgccttctaa---tctaattaaaagatgg-ttgagctttatgattgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA
|||| | |   | |||     ||||||    |||||   | | | |  | |   |  |   ||| | |     ||   ||   |||||   || ||| |||| ||||| || ||||||||  | ||||||||||||||||| ||||| ||||||||| | || ||||||||| | || |||||| | || |  ||||| |
gttacaaattctcatgaccagtcagattcatgaatatggtctgtatattacaaacagagattctgactgttctatctcttttactttacttttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACAGATGGAA

upper sequence: GRMZM2G012501_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 4
--------------------gttaaataaatgatgttttcagatgaatacaatgtttttgatgccttctaatctaattaaaagatggttgagctttatgattgt--aatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA
                     || | |  ||  | | |||   || ||    |||  |   ||  | ||||  |   | | | ||  |  | || | | ||| |  ||||||| ||||| |||||||||||  | |||||||||||||| |||||||  ||||||||||| || ||||| ||| |||| || ||| | || | ||| || |
gtttcattttcttatgcaacttttattttattttatattcttgtgtatggtctgtgatctgtgt-tactaacttggattataaatattctatctctttaatttttaaatagGTTATCATCGTCACAAGCTCTCTCATGAAGGACATGAACAGCAAGATTGATATGTACCGAGCAAATGCCATTCGAGTGCTGTGTCGTATCACTGACGGAA

upper sequence: GRMZM2G012501_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 4
gtta--aataaatgatgttttcagatgaatacaatgtttttgatgccttcta-atctaattaaaagatggttgagc-----------------tttatgattgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA
||||  |||   ||   ||||||   | |  ||   |     ||    |||  || | |  || |||   |    |                 ||||   || ||  |||| ||||| || ||||||||  | ||||||||||||||||| ||||| ||||||||| | || ||||||||| | || |||||| | || |  ||||| |
gttacaaattcttgcaattttcatgagcagtcagattcacgaatattgtctgtatatcacaaacagagattctgaccgttctatctcttttattttacttttttaccagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACGGATGGAA

upper sequence: GRMZM2G012501_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 4
----------gttaaataaatgatgtttt----cagatgaatac--aatgtttttgatgcctt---ctaatctaattaaaagatggttgagctttatgattgt--aatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA
           |||   || |  | ||||     ||||  || |  |  || | ||||   |    ||||  |   | | | ||  |  | || | | ||| |  ||||||| ||||| |||||||||||  | |||||||| ||||| |||||||  ||||||||||| || ||||| ||| |||| || ||| | || | ||| || |
gtttcattttcttatgcaacttttcttttattttagattcatgcgtatggtatgtgatctttattactaacttggattataaatattctatctctttaatttttaaatagGTTATCATCGTCACAAGCTCTCTCATGAAGGATATGAACAGCAAGATTGATATGTACCGAGCAAATGCCATTCGAGTGCTGTGTCGTATCACTGACGGAA

upper sequence: GRMZM2G012501_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 4
gttaaataaatgatgttttcagatgaatacaatgtttttgatgccttctaatctaattaaaagatggttga-gctttatgattgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA
|||||||  ||  |||| |   ||   |    |  |    |     | |     || |      ||||| |   |||||   |  || |||| || || || || |||||| | ||||||||||||||||||||||| |||||||| || || ||||||||| | ||||| ||| ||||||  ||||| |
gttaaattgat--tgttgttttatttgtttgtttgtaccaactttatttgtgaaaagtgctgactggtttataatttata--tacaaaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA

upper sequence: GRMZM2G012501_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------gttaaataaatgatgttttcagatgaatacaatgtttttgatgccttctaatctaattaaaagatggttgagctttatgattgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA
               ||| |||   ||| | |  || |    ||| | ||||     ||    |   | || | || ||     | |   |   |  |   |||| ||||| || |||||||| ||||||||||| ||||| |||||||||||  | || ||||| ||||| || || ||||| ||| |||| |  || ||| 
agcttgacatagagattagata--cgatatgtgaaggtctgaaca-ttttttcatgacccagaaggttgatcacaatattaaccaacagaagtctgattccagGTTATCATTGTGACAAGCTCTTTGATGAAGGATATGAACAGCAAGACAGACCTTTATCGTGCAAATGCCATAAGGGTTCTGTGTCGAATCACAGACGGTG

upper sequence: GRMZM2G012501_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S41_154V6.1 (Physcomitrella patens), 3'ss of exon 4
---gttaaataaatgatgttttcaga----tgaatacaatgt--ttttgatgccttctaatctaattaaaagatg-gttgagctttatgattgtaat--agGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA
    ||     || ||| || |||      || || || |||  |||  || | |||   |  | | |     |   ||||    |     | | ||  |||| || || || ||||||||||| |||||||| ||||| |||||||||||| | || || || || |||||  | || || || ||||| |  |||||| 
tgcattgtgccaa-gatcttatcaacattttgcatgcactgtattttctatactttcagttacagtcacgtattatattgacgagtgcatctctgatgcagGTTATTATTGTAACAAGCTCATTAATGAAGGATATGAACAGCAAGACAGATCTTTATCGCGCGAACGCTATACGGGTCCTCTGCAGAATCACAGATGGTG

upper sequence: GRMZM2G012501_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ15122 (Selaginella moellendorffii), 3'ss of exon 4
gttaaataaatgatgttttcagatgaatacaatgtttttgatgccttctaatctaattaaaagatggttgagctttatgattg-taatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA
                           ||   |  |    | |||||           ||| | |  || ||   ||   ||| | | |||| |||||||||||||||||  |||||||||||||||     ||||| ||| | ||||| || ||||| || || || |||||||| || |  |||||| 
--------------------------gtaagctcgtggaaacgcctttgg--------aaaggttttttaagacatagctttgctgacagGTTATCATAGTCACAAGCTCGCTGATGAAGGACATGAGCTCTAAGACGGATCTCTACCGAGCAAATGCAATAAGGGTGCTTTGTAGGATTACAGATGGTG

upper sequence: GRMZM2G012501_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ08461 (Selaginella moellendorffii), 3'ss of exon 4
gttaaataaatgatgttttcagatgaatacaatgtttttgatgccttctaatctaattaaaagatggttgagctttatgattg-taatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA
                           ||   |  |    | |||||           ||| | |  || ||   ||   ||| | | |||| |||||||||||||||||  |||||||||||||||     ||||| ||| | ||||| || ||||| || || || |||||||| || |  |||||| 
--------------------------gtaagctcgtggaaacgcctttgg--------aaaggttttttaagacatagctttgctgacagGTTATCATAGTCACAAGCTCGCTGATGAAGGACATGAGCTCTAAGACGGATCTCTACCGAGCAAATGCAATAAGGGTGCTTTGTAGGATTACCGATGGTG

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|89252140|gb|DY623926.1|DY623926
EST:     GGAGGTTAGTGTACTTAATGATGAAAGAACTTTCTCCATCGTCAGATGAG                         GTCATCATAGTCACAAGCTCCATTGATGAAGGACATGAATTAG-AGGACAG
genomic: GGAGGCTAGTGTACTTAATGATCAAAGAACTTTCTCCATCGTCAGATGAGgttaaataaa ... attgtaatagGTCATCATAGTCACAAGCTC-ATTGATGAAGGACATGAAT-AGCAAGACAG
EST: gi|148973647|gb|EE024760.2|EE024760
EST:     GGAGGCTAGTGTACTTAATGATCAAAGAACTTTCTCCATCGTCAGATGAG                         GTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGAT
genomic: GGAGGCTAGTGTACTTAATGATCAAAGAACTTTCTCCATCGTCAGATGAGgttaaataaa ... attgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGAT
EST: gi|76917670|gb|DV166948.1|DV166948
EST:     GGAGGCTAGTGTACTTAATGATCAAAGAACTTTCTCCATCGTCAGATGAG                         GTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGAT
genomic: GGAGGCTAGTGTACTTAATGATCAAAGAACTTTCTCCATCGTCAGATGAGgttaaataaa ... attgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGAT
EST: gi|67016076|gb|CO444825.1|CO444825
EST:     CGTCAGTTGAG                         GTCATCATAGTCACAAGCTCATTGATGAAGGACATGAACAGCAAGACAGAT
genomic: CGTCAGATGAGgttaaataaa ... attgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGAT
EST: gi|148970762|gb|EE021504.2|EE021504
EST:     GGAGGCTAGTGTACTTAATGATCAAAGAACTTTCTCCATCGTCAGATGAG                         GTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGAT
genomic: GGAGGCTAGTGTACTTAATGATCAAAGAACTTTCTCCATCGTCAGATGAGgttaaataaa ... attgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGAT
EST: gi|148967121|gb|EE018293.2|EE018293
EST:     GGAGGCTAGTGTACTTAATGATCAAAGAACTTTCTCCATCGTCAGATGAG                         GTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGAT
genomic: GGAGGCTAGTGTACTTAATGATCAAAGAACTTTCTCCATCGTCAGATGAGgttaaataaa ... attgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGAT
EST: gi|148946070|gb|EC891366.2|EC891366
EST:     GGAGGCTAGTGTACTTAATGATCAAAGAACTTTCTCCATCGTCAGATGAG                         GTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGAT
genomic: GGAGGCTAGTGTACTTAATGATCAAAGAACTTTCTCCATCGTCAGATGAGgttaaataaa ... attgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgatgccttctaatctaattaaaagatggttgagctttatgattgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA
           ttctaatctaattaaa  TA-rich tract