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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcaattcttacagtttgcatagtttgttgaatgtacttttacttttaccgtagtacaatgctcataatgtagaatactgtaaccagtttgcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG

Basic information

species Zea mays
transcript GRMZM2G050961_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050961_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g41710.1 (Oryza sativa), 3'ss of exon 4
gtcaattcttacagtttgcatagtttgttgaatgtacttttacttttaccgtagtacaatgctcataatgtagaatactgtaaccagtttgcacttg--------cagGTTCTCTTCTCAGACATCAATGCTTATGAG
        |||||||  ||| || | |||     |   ||   || || || | || ||||   ||     |  || |  | ||| | ||   ||||        |||||||||||||| ||||| ||||||||||||
------ctttacagtcggcacagct-gttccgcctgtgttc-tttgtatcgcattaaaatgtcaattgaacatgattcactgacctggttctgcttgtgactttgcagGTTCTCTTCTCTGACATAAATGCTTATGAG

upper sequence: GRMZM2G050961_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv15s0021g00830.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------------------------------------------------------gtcaattcttacagtttgcatagtttgt-tgaatgtacttttacttttaccgtagtacaatgctcata----atgtagaatactgtaaccagtttgcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
                                                                                          || ||||||   ||       | ||| | ||    || |   | ||||    || |  | ||||  ||    || || |  |  | ||    | |    ||||||||||| ||||||||||| ||||||||||||
gtaatgaatcataatggatcttctttttgttggtgttcttgtataaataattttttcagtgaattatttatattgatgccactgggactagtgaattctccaagaagctggactttctatgcgcttaatggcattttttttatattctagtgcttttataccatctaaaggaagggaatggctatctttttgcagGTTCTTTTCTCAGACATAAATGCTTATGAG
















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|13558469|gb|BG549825.1|BG549825
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|148943634|gb|EC888698.2|EC888698
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|211482968|gb|FK973427.1|FK973427
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGNTGGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTA
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGG-AAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTA
EST: gi|15198996|gb|BI423600.1|BI423600
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|148943633|gb|EC888697.2|EC888697
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|166466537|gb|EG225135.1|EG225135
EST:     AGATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: AGATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|29577011|gb|CB617123.1|CB617123
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|19058136|gb|BM736803.1|BM736803
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|211061029|gb|FL204116.1|FL204116
EST:     ATTCTATCGATCGGCGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|6342692|gb|AW165516.1|AW165516
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAG-CATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|29167933|gb|CB411193.1|CB411193
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|15499585|gb|BI596098.1|BI596098
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAA                         GATCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|19058714|gb|BM737381.1|BM737381
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GNTCTCTTCTCAGACATCAATGCTTATGAGGTGGAGCTTG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAGGTGGAGCTTG
EST: gi|13382241|gb|BG458916.1|BG458916
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|29947167|gb|CB816515.1|CB816515
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|211058063|gb|FL204109.1|FL204109
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|32849976|gb|CD989657.1|CD989657
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|13558470|gb|BG549826.1|BG549826
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|6431818|gb|AW172022.1|AW172022
EST:     ATTCTATCGATCGGTGCTGAAGTCAGNGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|13237244|gb|BG355258.1|BG355258
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|29544990|gb|CB605168.1|CB605168
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|26559456|gb|CA831691.1|CA831691
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaccgtagtacaatgctcataatgtagaatactgtaaccagtttgcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
                                ctgtaac  putative branch site (score: 3)
                   ataatgta  TA-rich tract