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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctttattatcacttcatatttatcataatctgttctttctttttcatctgcatggaattttaggttgattcctcgattttgtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTATACCAGCATATTGTCGCTATGCAGAAAG

Basic information

species Arabidopsis thaliana
transcript AT4G26430.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os08g39070.1 (Oryza sativa), 3'ss of exon 5
------gtaagctttattatcacttcatatttatcataatctgttctttctttttcatctgcatggaatttt--aggttgattcc--tcgat---tttgtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTATACCAGCATATTGTCGCTATGCAGAAAG
      ||     |||| |||| || || | |  || |   ||   | |  |   ||  |  || |  |||   |   |||| |     |||   |||| ||||||||||||||||| || |||||||| ||||||||||||||||| ||||||||  || | ||  |  | ||  || ||||  | ||||||||||
gtgagggttcttcttatcatcagtttatgtcttacagatattgagttgtactacccaa-tatattgtttttggaaaaatgatactgacagatatatttgagcagTGGCTGCTCATCTGACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAATATCTTGTTTCCATGCAGAAAG

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------gtaagctttattatcacttcatatttatcataatctgttctttcttt-------ttcatctgcatggaattttaggttgattcctcgattttgtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTATACCAGCATATTGTCGCTATGCAGAAAG
                                                   |    |||     |  |||    ||    | ||   ||  | |  |        ||  |||| || ||| | ||     |  |   | |||||||||||||||||||||||||| |||||||| ||||||||||||||||| ||||||||  || | ||  |  | ||| || |||| || ||||| ||||
gtaagcattctactttgaagccctctctcaaaacaaatttatgggtcagtgggtgtcttccccgtggctttgctttctcaacaaatagtcatattatccgaggtatttttctggatagaaatgta---ctaaacgatgcttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G080652_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------gtaagctttattatcacttcatattt-----atcataatctgttctttct----ttttcatctgcatggaattttaggttgattcctcgattttgtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTATACCAGCATATTGTCGCTATGCAGAAAG
                                           |    |||   | |  |||    ||      || || |    | || |||    | |   |||| |  ||||| ||     | ||   ||||| |||||||||||||||||||||| |||||||| ||||||||||||||||| ||||||||  || | ||  |  | ||| || | || || ||||| ||||
gtaagagttataatttgaagacatctcataagacagccctgggggtgtcttccctgtggctttgctttctcaacattattagtcatactgtctgaggtatatttctggacagaattgta---ctaatcgatgatttcgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 5
------gtaagctttatta-tcacttcatatt-tatcataatctgttctttctttttcatctgcatggaattttaggttgattcctcgatttt---gtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTATACCAGCATATTGTCGCTATGCAGAAAG
       | |    | | | | ||| ||  |  |    |||  |||   || ||||  |  || || | || |       |||||  | |||     ||||||||||||||| |||||||||||||| ||||||||||| |||||| |||||||||| |  |||||| | ||  || || | || ||||| ||||
tgttgattgatgcatgtaagtgactccacctagtggggtaaggtgtgggttttttt--agttgtattgcatgtatctaatattccatgttttcttaatgcagTGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACATCACTATCTTCTTGCAATGCAAAAAG

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 5
------gtaagctttattatcacttcatatttatcataatctgttctttctttttcatctgcatggaattttaggttgattcctcgattttgt---gcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTATACCAGCATATTGTCGCTATGCAGAAAG
      ||    |    ||   |     |  ||     ||  ||| |   ||||| |  |  ||   || |       |||||  | |||  |    ||||||||||||| |||||||| | ||| ||||||||||| |||||| |||||||||| |  |||||| ||||  || || | || ||||| ||||
aatgttgttgattgatgtaagtcactgcacctagtgggattagttgtgatttttttagttttattttatgtatctaatattccatgttttcttattacagTGGCTGCTCACCTTACTGGTACACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACACCACTATCTTCTTGCAATGCAAAAAG

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------------------gtaagctttattatcacttcatatttatcataatctgttcttt-ctttttcatctgcatggaatttta-ggttgattcctcgatt----------ttgtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTATACCAGCATATTGTCGCTATGCAGAAAG
                                                                   || | ||  |  | ||  |||   |   |||   |  | | | ||||  |  | |   ||| ||  |  ||  |   | | |          ||||||||||||||| || || || || ||||||||||||||||||||||| |||||||||||| | || ||  | ||  || |  | |||||||| ||||
gtaagcccttatctccaccatcatttcttgtcttgtctcttaccatttttgcagaaaattataaactagttctac-agaagtttttatccttttcaatacatattatgcatttttttaagaaaaaaatcttgtgaatggctttacaactgtggctatgtttgtgcagTGGCTGCCCACCTCACGGGGATACATAGTGCCATCAAGATGCTAAATAGCAGAATCCGTGTTCTTCATCATTATCTGCTTGCTATGCAAAAAG

upper sequence: AT4G26430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S34_439V6.1 (Physcomitrella patens), 3'ss of exon 5
-gtaagctttattatcacttcatatttatcataatctgttctttctttttcatctgcatggaattttaggttga---ttcctcgattttgtg-------cagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTATACCAGCATATTGTCGCTATGCAGAAAG
 | | |  || | |     | || |  ||   | |||||   |   |    |   || |||  ||    ||| |   ||  | | | |||||       |||| ||||||||| | || || || ||||||||||| ||||||||||||||||| ||  ||||  |||| || ||  |||   |||| |||||||
tggatgtattttgaaggaatgatgtc-attgca-tctgtcactgtctaacaaatggcgtggttttcacagttaaaattttgtgggtcttgtggttgctgcagTTGCTGCTCATTTGACCGGGATGCATAGTGCCATAAAGATGCTTAATAGCAGGATTCGAGTTTTATATCACCACCTTGCTTCTATTCAGAAAG

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|116443196|gb|EG485788.1|EG485788
EST:     TCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT                         TGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGTA
genomic: TCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagcttta ... ttttgtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCA
EST: gi|86080018|gb|DR375775.1|DR375775
EST:     TCATG-TGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT                         TGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCA
genomic: TCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagcttta ... ttttgtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCA
EST: gi|164060170|gb|ES187667.1|ES187667
EST:     TTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT                         TGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAA
genomic: TTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagcttta ... ttttgtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAA
EST: gi|116443197|gb|EG485789.1|EG485789
EST:     TCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGT                         TGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGTA
genomic: TCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagcttta ... ttttgtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctttctttttcatctgcatggaattttaggttgattcctcgattttgtgcagTGGCTGCTCATCTTACTGGAATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTATACCAGCATATTGTCGCTATGCAGAAAG
                               ggttgat  putative branch site (score: 5)
                        aatttta  TA-rich tract