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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcatgcagctatgttataccttattatccatatatactgattccgttaccgttgtcaatactccatgtacagtattggtatgccaatcatatttggataatctaataagctcatgctgttcctcttctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTG

Basic information

species Zea mays
transcript GRMZM2G046816_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046816_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g06420.1 (Oryza sativa), 3'ss of exon 2
------------------------------------------------gtaatcatgcagctatgttatac-cttattatccatatatactg-----attccgt--taccgttgtcaatactccatgtacagtattggtatgccaatcatatttggataatctaataagctcatgctgttcctcttctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTG
                                                 ||    | |  | ||||||    ||| |  | || | ||| ||     ||| ||    ||     |  | |   ||   ||| |||||  | |   | | | |    |||  |||||||| ||||| | |||| ||||| | ||||||||||||| |||||||||||||| |||||||| |||| ||||||||  ||||| || | ||||  | |||||||   | || ||||||
gtgatcatgcaaattgtgttgtttttagttttatatcctttacaagcaatatcagttcgtccatgttaggtgcttgtccttca-acatattgttggaatttcgaaacacaaaaatagaaagaacacccaca-tattg-caggattaccgtttgcttatatgctaataagttcatgttattccgcttctatgtacagCCTGGGCCACGAGATGGAACTATGCAGTGTTTCATTAGGAGGGATAAGTCTACGCAGACCTACTATTTGTACCTCTCTCTTGGCTCTG

upper sequence: GRMZM2G046816_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g06420.2 (Oryza sativa), 3'ss of exon 2
----------------------------------------------------gtaatcatgcagctatgttatac-cttattatccatatatactg-----attccg--ttaccgttgtcaatactccatgtacagtattggtatgccaatcatatttggataatctaataagctcatgctgttcctcttctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTG
                                                     ||    | |  | ||||||    ||| |  | || | ||| ||     ||| ||    ||     |  | |   ||   ||| |||||  | |   | | | |    |||  |||||||| ||||| | |||| ||||| | ||||||||||||| |||||||||||||| |||||||| |||| ||||||||  ||||| || | ||||  | |||||||   | || ||||||
gcaggtgatcatgcaaattgtgttgtttttagttttatatcctttacaagcaatatcagttcgtccatgttaggtgcttgtccttca-acatattgttggaatttcgaaacacaaaaatagaaagaacacccaca-tattg-caggattaccgtttgcttatatgctaataagttcatgttattccgcttctatgtacagCCTGGGCCACGAGATGGAACTATGCAGTGTTTCATTAGGAGGGATAAGTCTACGCAGACCTACTATTTGTACCTCTCTCTTGGCTCTG

upper sequence: GRMZM2G046816_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 1
gtaatcatgcagctatgttataccttattatccatatatactgattccgttaccgttgtcaatactccatgtacagtattggtatgccaatcatatttgg-ataatctaa---taagctcatgctg-ttcctcttctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTG
                                                 |||  |       |  |   || | || |    | | ||| | ||||| || ||   |||    | | ||  | ||| ||  | |  ||| ||||||| |||||||| |||||||| |||||||| || ||||||||||| |  || | |   |  |||   || | |||| |  ||||| |||
------------------------------------------------cttaaaggctcatgtgtttgttgaaaagaaagaatttccca-ttatattggggatgggctatgattgacctagttctggtttgtttgttgtttacagccagGGCCTCGGGATGGAACCATTCAGTGCTTCATTAAGAGGGACAAGTCCAACTTGACTTACCACCTTTTCCTTTGCCTTAGCCCTG

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|31360425|gb|CD444782.1|CD444782
EST:     AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAG                         CCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATAAATCT
genomic: AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgc ... ctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT
EST: gi|67042292|gb|CO468547.1|CO468547
EST:     CTGTTT-CTTGCAA-CAG                         ACTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATATTTC
genomic: CTGTTTCCTTG-AAGCAGgtaatcatgc ... ctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATC
EST: gi|211214115|gb|FL021289.1|FL021289
EST:     GAGCCCAGAGTTTTCTGGAAAAATCACTTTTTCCTGTTTCCTTGAAACAG                         CCCTGGGCCTCCAGATGGAACTATTCAGTGGTTTA
genomic: GAGCCCAGAGTTTTCTGGAAAAATCACTTTT-CCTGTTTCCTTGAAGCAGgtaatcatgc ... ctgtctacagCC-TGGGCCTCGAGATGGAACTATTCAGTGTTTTA
EST: gi|22819363|gb|BU499453.1|BU499453
EST:     AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAG                         CCTGGGCCTCGAGATGGAACTATTCAG-GTTTTATTAAGAGGGATACATCT
genomic: AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgc ... ctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT
EST: gi|26559903|gb|CA832138.1|CA832138
EST:     AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAG                         CCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT
genomic: AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgc ... ctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT
EST: gi|29130559|gb|CB381263.1|CB381263
EST:     AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAG                         CCTGGGCCTCGAGATGGAACTATTCA
genomic: AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgc ... ctgtctacagCCTGGGCCTCGAGATGGAACTATTCA
EST: gi|87156288|gb|DY401077.1|DY401077
EST:     AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAG                         CCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT
genomic: AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgc ... ctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT
EST: gi|74238493|gb|DT646407.1|DT646407
EST:     AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAG                         CCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT
genomic: AGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgc ... ctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccaatcatatttggataatctaataagctcatgctgttcctcttctgtctacagCCTGGGCCTCGAGATGGAACTATTCAGTGTTTTATTAAGAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTG
                  atctaat  putative branch site (score: 3)
                                  ctgttcctcttctgtc  putative PPT
               ataatctaataa  TA-rich tract