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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttagtgaatgagaaaccgaaactaaaagtcactacagtattggctatctcctctgttgtttcatccttttaatgtttatataatatctatatcttttctggtttatcagGTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G19990.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G107362_T03 (Zea mays), 3'ss of exon 3
gtatgcttagtgaatgagaaaccgaaactaaaagtcactacagtattggctatctcctctgttgtttcatccttttaatgtttatataatatctatatcttttctggtttatcagGTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAG-------------------------------------
                                             || | | |   ||     |     || ||  ||| |  | ||  |    || | |   ||    | ||||||||||||||| |||||||| ||||| ||| ||||||||   |||||||||||||| ||||||                                     
--------------------------------------------gtttgttttgaactaaaaagcactgtcattaaaatatgcacattctg---atttgtgaactcaactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAGGTTTGTTTTCTTTTTTGAAGACCATCTTAACCTTTTG

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 3
gtatgcttagtgaatgagaaaccgaaactaaaagtcactacagtattggctatctcctctgttgtttcatccttttaatgtttatataatatctatatcttttctggtttatcagGTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAG
                                             || | | |   ||     |     || ||  ||| |  | ||  |    || | |   ||    | ||||||||||||||| |||||||| ||||| ||| ||||||||   |||||||||||||| ||||||
--------------------------------------------gtttgttttgaactaaaaagcactgtcattaaaatatgcacattctg---atttgtgaactcaactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTGTTTGAGAGCCTTGGAATTGCGCAACCAAAG

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 3
gtatgcttagtgaatgagaaaccgaaactaaaagtcactacagtattggctatctcctctgttgtttcatccttttaatgtttatataatatctatatcttttctggtttatcagGTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAG
                                             || | | |   ||    ||    |||     ||| |  | ||  |    || | |   |     | ||||||||||||||| |||||||| ||||| ||| | ||||||   ||||||||||| || ||||||
--------------------------------------------gtttgttttgaactaaaatgcagtatcaccaaaatatgcacattctg---atttgtgaacacaactttcagGTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------gtatgcttagtgaatgagaaaccgaaactaaaagtcactacagtattggctatctcctc-tgttgtttcatccttt--taatgtttatataatatctatatct----tttctggtttat----cagGTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAG
                                                     |||| |      || |  |||    |     |    ||      |   ||| |  |  ||| |  |||| | ||   ||  ||  | || | | |  | ||    | | || || |     |||||||||||||| |||||||| ||||||||  |||||||   |||||||||||| || ||||||
gtactttgcttgacattctttcaatgtcaggagttagatgcttttatctatccatgcatcactcgtgtgttaccttt-ccgtgtgcatgtatctatctatttatattttagtgtagcatcatgcattagaaaaattagtttagtttttgaacctaatgtatgtgattaaatgtacagGTCATTGAGCTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------gtatgcttagtgaatgagaaaccgaaactaaaagtcactacagtattggctatctcctc-tgttgtttcatcctttt--aatgtttatataatatctatatct----tttctggtttat----cagGTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAG
                                                                           |||| |      || |  |||    ||  | |    ||   |||    ||| |  |  ||| |  |||| | ||   ||  |   | || | | |    ||    | | || || |     |||||||||||| | |||||||| ||||||||  |||||||   |||||||||||| || ||||||
gtatgttgcttgacattctttcggttttggcatttaaaattcgttctgtcaggagttagatattcttacctatccatgcatcactcgtgtgttaccttc-ctgtatgcatgtatc-tatcatgtatattttagtgtagcatcatgcattacaaaaatccgtttagtttttgggcctaatgtatgtgattaaatgtacagGTCATTGAGTTACCAATCAAACATCCTGAGCTGTTTGAAAGTCTTGGAATTGCACAACCAAAG

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------------------gtatgcttagtgaatgagaaaccgaaactaaaagtcactacagtattg-gctatctcct-ctgttgtttcatccttttaatgtttatataatatctatatcttttctggtttatcagGTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAG
                                                               ||   | | | ||      |   ||| |   | ||  || |  |    | ||||||    | || |||  || ||||   |||||  |  | | | |   | |  || | | ||||||||||||||| ||||| || || |||||| ||||||||  ||||||||| || || ||||||
gtttgtcctttgaccaattcttacatgttatttcattattattattaccattagcagcacttttaccttgatttaagttaggatttaaattcttaatctatagataagaaaggtatctcagatttttattttctcattttg--gtttaccttgtttttgt---tgtcttgatctttcagGTCATTGAGCTTCCAATTAAACACCCTGAACTGTTTGAGAGTCTTGGAATAGCTCAACCAAAG

upper sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 3
gtatgcttagtgaatgagaaaccgaaactaaaagtcactacagtattggctatctcctctgttgtttcatccttttaatgtttatataatatctatatcttttctggtttatcagGTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAG
                                  |  ||| | |    ||| ||| ||   || |||  |    || |  |   | |      |||    | |        |||||| |||||||| |||||||||||||||||||| |||||   |||||| || || || ||||||
--------------------------------gttagctata-tgagagct-tcttctgatttatttgttttggttgaaatccttctgt--cttatgctgtcttaaacccttcagGTTATTGAGCTTCCAATCAAGCATCCTGAATTATTTGAAAGTCTTGGTATAGCTCAACCAAAG

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|301502412|gb|HO207952.1|HO207952
EST:     CCTATGACATGATTGGTGGTCTTGACCAGCAGATTAAGGAAATAAAGGAG                         GTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATT
genomic: CCTATGACATGATTGGTGGTCTTGACCAGCAGATTAAGGAAATAAAGGAGgtatgcttag ... ggtttatcagGTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATT
EST: gi|124760229|gb|EH850359.1|EH850359
EST:     GTCTTGACCAGCAGATTAAGGAAATAAAGGAG                         GTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATT
genomic: GTCTTGACCAGCAGATTAAGGAAATAAAGGAGgtatgcttag ... ggtttatcagGTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATT
EST: gi|125046109|gb|EL118378.1|EL118378
EST:     CCTATGACATGATTGGTGGTCTTGACCAGCAGATTAAGGAAATAAAGGAG                         GTCATTGAGCTGCCAATCAAGCATCCTGAAT
genomic: CCTATGACATGATTGGTGGTCTTGACCAGCAGATTAAGGAAATAAAGGAGgtatgcttag ... ggtttatcagGTCATTGAGCTGCCAATCAAGCATCCTGAAT
EST: gi|124940718|gb|EL017144.1|EL017144
EST:     CTTGACCAGCAGATTAAGGAAATAAAGGAG                         GTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATT
genomic: CTTGACCAGCAGATTAAGGAAATAAAGGAGgtatgcttag ... ggtttatcagGTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATT
EST: gi|164221424|gb|ES019712.1|ES019712
EST:     TTGGTGGTCTTGACCAGCAGATTAAGGAAATAAAGGAG                         GTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATT
genomic: TTGGTGGTCTTGACCAGCAGATTAAGGAAATAAAGGAGgtatgcttag ... ggtttatcagGTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtttcatccttttaatgtttatataatatctatatcttttctggtttatcagGTCATTGAGCTGCCAATCAAGCATCCTGAATTGTTTGAGTCTCTTGGAATTGCGCAGCCAAAG
            ttttaat  putative branch site (score: 3)
                                     tcttttctg  putative PPT
        atccttttaatgttta  TA-rich tract