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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCAGCGGCTGGGAGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcagcgcactcgcttggtcgatcccacgttgtttctgttcgtgcaggttgtagagataggattctcgctgatttgttcatgttttggttaggag...

Basic information

species Zea mays
transcript GRMZM2G152573_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152573_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA01G05740.1 (Glycine max), 5'ss of exon 1
GAAGCAGCGGCTGGGAGC-AAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaa---gatcag---cgcact-----cgctt--ggtcgatcccacgtt-gtttctgttcgtgcag-gttgtagagataggattctcg---ctgatttgttc--------atgttttggttaggag----------------
||| | | |||||||||||||| ||||||||||| |||||||||||||| |||||||| || ||||| | | |||||||| || |||||||| ||| | |||| |||| | ||| | | || |||| |||| || ||| || | | | || | | | ||| |||| | || ||| || |
-GAGCGTGATCCATTGACGAAGATGGTGCAGCGTCTCACCTACCGCAAGCGGCACAGCTATGCCACCAAGTCCAACCAACACAGGGTCGTCAAAACCCCTGgtaatcaaatccctccctcactgattatgcttcggatcggaacaatttttgtttttgtttttgttttgttttaaaaaaaaagtttttggtattaattggttctgctgggtacgtcttgtttggttctgtgggaataatgcag

upper sequence: GRMZM2G152573_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA08G41280.1 (Glycine max), 5'ss of exon 1
-GAAGCAGCGGCTGGGAGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcagcgcactcgcttggtcgatcccacg--ttgtttctgttcgtg-caggttgtagagataggattct-cgctgattt---gttcatgttttggttaggag--------------------
|||| ||| | | |||| |||||||||||||| ||||||||||| ||||| |||||||| ||||||||||| |||||| | | ||||||||||| || ||||| | ||||| | | | || || || | | ||||| | | | | || | | || |||| | | |
GGAAGAAGCTGATCGGAG-AAGATGGTGCAGCGTCTCACCTACCGCAAGCGCCACAGCTATGCCACCAAATCCAACCAGCACAGAGTCGTCAAGACTCCCGgtaaataaactctcttcgctcgcctcacatcgtcgtttattctcactcacggcgcgttgtcgttttgcgccgccgcgagggctccaaaaatatattttaatgtgcggttgctgattgttgaatgcag

upper sequence: GRMZM2G152573_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA18G14980.1 (Glycine max), 5'ss of exon 1
-GAAGCAGCGGCTGGGAGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcagcgcactcgcttggt-cgatcccacgttgtttctgtt--cgtgcaggttgtagagataggattctcg---ctgatttgttcatgttttggttaggag----------
|||| ||| | | ||| |||||||||||||| ||||||||||| || || |||||||| || |||||||| |||||| | | ||||||||||| || ||||| | | ||||||| | || || | || | |||| | ||| | || |||| || | || ||| | | |
GGAAGAAGCTGATCCGAG-AAGATGGTGCAGCGTCTCACCTACCGCAAACGCCACAGCTATGCTACCAAATCCAACCAGCACAGAGTCGTCAAGACTCCCGgtaaactgtcttcgctcgcttcgcatcgtcgtttattctcactcatggcgtgtcgtttgcgccgcgagtgttctaaaaatagactgtaatgtgcggtggctggttgttgaatgcag

upper sequence: GRMZM2G152573_T04 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA02G11920.1 (Glycine max), 5'ss of exon 1
GAAGCAGCGGCTGGGAGC-AAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcagcgcactcgcttggtcgatcccacgttgtttctgttcgtgcaggttgtagagataggattctcgctgatttgttc---atgtt--ttggttaggag------------------------------------
||| | | |||||||||||||| ||||||||||| ||| |||||||||| ||||||||||| ||||| | | |||||||| || |||||||| ||| | ||| | || | ||| | | | | ||| | | | | | ||| | ||| || || | || |||||| ||
-GAGCGTGATCCATTGACGAAGATGGTGCAGCGTCTCACCTACCGCAAGAGGCACAGCTATGCCACCAAATCCAACCAACACAGGGTCGTCAAAACCCCTGgtaa--tcaaatccctc-ttcggaacccctcactcactcttcgattatgct--tcgaatcggaacaatttttgctttttaattttgggtattaattggttctgacgggtatgttgtgtttggtgatgtgggaataatgcag

upper sequence: GRMZM2G152573_T04 (Zea mays), 5'ss of exon 1
lower sequence: AT1G26880.1 (Arabidopsis thaliana), 5'ss of exon 1
GAAGCAGCGGCTGGGAGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcagcgcactcgcttggtcgatcccacgttgtttctgttcgtgcaggttgtagagataggattctc-----gctgatttgttcatgttttggttaggag---------------------
|| || | | || ||||||||||| || |||||| ||| ||||||||||||||||||||||||||| ||| |||||||||| || ||| | || ||| || | || | | | | || | | ||| | |||||| | ||| ||||| | | || | | |
AAAAGAGAAAAGGAGGCGAAAATGGTGCAGCGTCTTGTTTACCGGTCGCGACACAGCTACGCCACCAAATCGAACCAGCACCGTATCGTCAAGACTCCAGgtccctttcttcttctt-cttcttc--ttccttgatatcttcaatctcctctgctttagtctcataattctctaatcaccgatctgttcttcatagtgtaatgtgtgttgggattgttgatttcag

upper sequence: GRMZM2G152573_T04 (Zea mays), 5'ss of exon 1
lower sequence: Vv14s0108g00850.t01 (Vitis vinifera), 5'ss of exon 1
-GAAGCAGCGGCTGGGAGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcagcgca-----ctcgcttggtcgatcccacgttgtttctgttcgtgc---aggttgtagagataggatt-ctcgctgatttgttcatgttttggttaggag
| || | | || | || ||||| ||||| ||||| ||||| || ||||| ||||| ||||||||||| |||||| | | |||||||| || |||||| | | | || | || || | | | | ||| | | | || || | | | | | | |||| | | ||| ||
GGGAGGTGAGAGTGCTTG-AAAATGGTCCAGCGTCTCACATACCGCAAACGGCATAGCTATGCCACCAAATCTAACCAGCACAGGGTCGTCAAAACCCCTGgtgattcttctgtaaaacccttggtttttcttttcttcagtattttattgcatctgttagtttatttgggtgatttggtttgttgatcggaacgtgtatt---------

upper sequence: GRMZM2G152573_T04 (Zea mays), 5'ss of exon 1
lower sequence: PP1S76_47V6.1 (Physcomitrella patens), 5'ss of exon 1
GAAGCAGCGGCTGGGAGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcagcgcactcgcttggtcgatcccacgtt------gtttctgttcgtgc---aggttgtagagataggattctcgc------tgatttgtt--catgttttggttaggag------------------------------------------
| | | || || ||||||||||| | |||||| || ||| ||| |||| ||||||||||| |||||||| || || |||||||| |||||| ||| | | | | | || | |||||| |||| || || || | | | | || ||| ||| ||| | |||
TGTGTGGGGTGGGGTGACACCATGGTGCAGCGTTTGACCTACAGGCGGCGCCACTGCTATGCCACCAAATCCAACCAGACTCGTGTGGTCAAGACCCCTGgtgagagtctctcccccttctcttccagtgcacgttttaggagttttaccccgcatcgaagctttttacggtgaattgaatgcaagggatgaggcgttattatggaccaatcgagagttgatgtctggattgagctttgcgttgttttgtgggatatag

upper sequence: GRMZM2G152573_T04 (Zea mays), 5'ss of exon 1
lower sequence: PP1S200_25V6.1 (Physcomitrella patens), 5'ss of exon 1
GAAGCAGCGGCTGGG--AGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcagcgcactcgcttggtcgatcccacgttgtttctgttcgtgcaggttgtagagataggattctcgc-tgatttgttcatgttttggttaggag----
| | |||| || ||||| ||||| | || ||||| || ||| |||| |||||||| ||||||||||||||||| |||||||| || |||| || || || || || | | || ||||| | | | | || | ||| || | | | || |||| || |
--GCTATCTCCTGGTCTGTCACCATGGTTCAGCGATTAACGTACCGTCGCCGCCACTGCTATGCCACCAAGTCGAACCAGACCCGCGTGGTCAAGACCCCAGgta----cactgccttccctctctctttgtcgcgaattttctaggc-tacggatttcggcttagatatttcggcatcgtgttttggggtttggggccagcattgt

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|211379329|gb|FL156716.1|FL156716
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|15208979|gb|BI430863.1|BI430863
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211379330|gb|FL156717.1|FL156717
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1062

GAAGCAGCGGCTGGGAGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGTGCCCAGTCACCGGGAAGAAGATCCAAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1147

GAAGCAGCGGCTGGGAGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGTGCCCAGTCACCGGGAAGAAGATCCAAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1151

GAAGCAGCGGCTGGGAGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGTGCCCAGTCACCGGGAAGAAGATCCAAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 673

GAAGCAGCGGCTGGGAGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGTGCCCAGTCACCGGGAAGAAGATCCAAGGA