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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattgacagaactgccagtttagatatgcatttaattattgagttatgttctgagccgattcatattttttctggttacctgattactgtcctctatacatgtaatgtgatgacttctgttttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGAT

Basic information

species Zea mays
transcript GRMZM2G177970_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177970_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g54020.1 (Oryza sativa), 3'ss of exon 10
gtgattgacagaactgccagtttagatatgcatttaattattgagttatgttctgagccgattcatattttttctggttacctgattactgtcctctatacatgtaatgtgatgacttctgttttg-------gtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGAT
                                   | ||   ||| |   |||   ||  ||  ||||||| |     |  ||| | | ||| || ||||  | |    |  |||| | |||| ||        || |||||||| ||||||||||||||||| ||||||||||||||||||||||| |||||||||
----------------------------------aacttgcagagctg-attccaggc--atctatattttat---actttctgctcagtgtgctgtatatctctgccatactgacctttgttctgtttattcatgttagATGTCGAAGTCTGCTCCTTCAGATCAGTCTCGTATTAACCTTCTTGATCCAAAAGAT

upper sequence: GRMZM2G177970_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT2G25840.2 (Arabidopsis thaliana), 3'ss of exon 8
gtgattgacagaactgccagtttagatatgcatttaattattgagttatgttctgagccgattcatattttttctggttacctgattactgtcctctatacatgtaatgtgatgacttctgttttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGAT
                           |   ||  |||| ||| | |   || |       |||| ||  |     |  |  | || |||   | |||      || ||| |||       | |||    ||||||||||||||||| ||||| || ||||| || ||||| || |||||| ||||||||
------------------------tgaactaatccaatttttgggcttacttattgttgttttcaaatgatcaagaggaattttat-acttatcgctaaggtcttactgtcatg----taatcttg----tagATGTCCAAGTCTGCCCCTTCTGATCAGTCCCGGATTAATCTCCTTGACTCAAAAGAT

upper sequence: GRMZM2G177970_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv04s0008g00200.t01 (Vitis vinifera), 3'ss of exon 10
gtgattgacagaactgccagtttagatatgcatttaattattgagttatgttctgagccgattcatat-tttttctggttacctgattactgtcctctatacatgtaatgtgatgacttctgttttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGAT
                    ||  ||| |  |||  |   |    |||| ||||       |  ||   ||| | | ||||||  || ||  | |  | | |||             || |  ||||    |||||||||||||||||| ||||||| ||||||||||| |||||||||||||||||||||
-------------------cttctgatgtctattagacc-tctctttat-ttctacttttgtaaatgggtttcttttgttaccgaatgacaattcctttttcat-------------ttttcgtttgtctgtagATGTCCAAGTCTGCTTCTTCAGATCAGTCTCGTATCAACCTTCTTGACCCAAAAGAT

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|76012104|gb|DT939274.1|DT939274
EST:     TTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAG                         ATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCA
genomic: TTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAGgtgattgaca ... ttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCA
EST: gi|78120427|gb|DV538811.1|DV538811
EST:     TTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAG                         ATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCA
genomic: TTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAGgtgattgaca ... ttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacctgattactgtcctctatacatgtaatgtgatgacttctgttttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGAT
 acctgat  putative branch site (score: 4)
                                     cttctgtttt  putative PPT
                  tatacat  TA-rich tract