Sequence
atgc intronic sequence ATGC exonic sequencegtaaatcaattcctttctgaactttaggttcctgtatgctgcttattttattgttaaatattttgtattgtttgcagATAGAGGTTGAAACCGTTGATAGAACTGGAACGTTCTTGGGATCCTTATGGGAGTCGAGGACCAATGTGGCAATTACACTGCTTGAAGCTGGTCTTGCAA
Basic information
species | Glycine max |
transcript | GLYMA04G38010.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G38010.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 11
gtaaatcaattcctttctgaactttaggttcctgtatgctgcttattttattgt-taaata-ttttgtattgtt-tgcagATAGAGGTTGAAACCGTTGATAGAACTGGAACGTTCTTGGGATCCTTATGGGAGTCGAGGACCAATGTGGCAATTACACTGCTTGAAGCTGGTCTTGCAA
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-----gtatgactcttgtgcatctttggttaatccacctccatggcttcgatgtctaaataataccatgtgattctacagATAGAGGTTGAAGCAGTTGATAGAACTGGGACATTCTTAGGTTCCTTATGGGAGTCCAAAACCAACATGGCTTCTGTTCTTCTGGAGGCTGGTCTGGCCA
upper sequence: GLYMA04G38010.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os04g32960.1 (Oryza sativa), 3'ss of exon 11
--------------------gtaaatcaattcctttctgaactttaggttcctgta--tgctgcttattttattgt-taaatattttgtattg-tttgcagATAGAGGTTGAAACCGTTGATAGAACTGGAACGTTCTTGGGATCCTTATGGGAGTCGAGGACCAATGTGGCAATTACACTGCTTGAAGCTGGTCTTGCAA
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tttcatccattaggattaatgttgggct-ctcctaggagagccttcaatcagtataattaaaattgttttcattttctaagaattttgaatgactttgcagATTGAGATCAACACAGTTGATAGAACTGGAACATTCTTAGGTTCCTTATGGGAATCTAATATCAATGTGGCTTCGGTTCTTTTGGAGGCTGGTCTTGCTA
upper sequence: GLYMA04G38010.1 (Glycine max), 3'ss of exon 12
lower sequence: AC207890.3_FGT002 (Zea mays), 3'ss of exon 11
gtaaatcaattcctttctgaactttaggttcctgtatgctgcttatttta--ttgttaaatat-tttgtattgtttgcagATAGAGGTTGAAACCGTTGATAGAACTGGAACGTTCTTGGGATCCTTATGGGAGTCGAGGACCAATGTGGCAATTACACTGCTTGAAGCTGGTCTTGCAA
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----gtacaactttagctgt-ctcttggttcttccatttccccattttcagtttctgaaggatgcaagtggtacatgcagATAGAGGTTGAAGCAGTTGATAGGACAGGAACGTTCATAGGTTCTTTGTGGGAGTCCAAGACCAACATGGGCTCTGTGCTTCTGGAAGCTGGACTTGCCA
upper sequence: GLYMA04G38010.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G07350.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaaatc-aattcctttctgaactttaggttcctgtatgctgcttattttattg--ttaaatattttgtattgtt----tgcagATAGAGGTTGAAACCGTTGATAGAACTGGAACGTTCTTGGGATCCTTATGGGAGTCGAGGACCAATGTGGCAATTACACTGCTTGAAGCTGGTCTTGCAA
||||| | ||| | ||| | ||| | | || | || | ||| | || || || | |||| | ||||| || ||||||||||| |||||||| || || |||||||||||| | ||||| |||||||| || ||||| | |||||||||||||| | ||||
gtaaaccgaatgcacatctaagaattaa-tctcagtttcctattcttttaaatgggtttctcatactctattataatcacacagATTGAAGTTGAAACCGTGGATAGAACCGGTACTTTCTTGGGATCCATGTGGGAATCGAGGACAAACGTGGCTACAGTTCTGCTTGAAGCTGGCTTAGCAA
upper sequence: GLYMA04G38010.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0283g00020.t01 (Vitis vinifera), 3'ss of exon 12
gtaaatcaattcctttctgaactt-taggttcctgtatgctgcttat---tttattgttaaatattttgtattgtttgcagATAGAGGTTGAAACCGTTGATAGAACTGGAACGTTCTTGGGATCCTTATGGGAGTCGAGGACCAATGTGGCAATTACACTGCTTGAAGCTGGTCTTGCAA
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--gtactgttcctcttttaaactggtaacctgctggctggtttctttccctttgttgctaaatctattctttcttatgcagATTGAAGTGGAAACTGTTGATAGAACTGGAACTTTCTTGGGATCTCTATGGGAGGCAAAAACCAACATGGCAGTGACACTTCTTGAGGCTGGACTAGCAAMapped 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|254326210|gb|GR840802.1|GR840802EST: ACGAAGCAATTGCTCTGATGAGGAGAAAGATAATGCAAAGAGATGTTGAG ATAGAGGTTGAAACCGTTGATAGAACTGGAACGTTCTTGGGATCCTTATGG
genomic: ACGAAGCAATTGCTCTGATGAGGAGAAAGATAATGCAAAGAGATGTTGAGgtaaatcaat ... ttgtttgcagATAGAGGTTGAAACCGTTGATAGAACTGGAACGTTCTTGGGATCCTTATGG
EST:
gi|298165137|gb|HO011186.1|HO011186EST: ACGAAGCAATTGCTCTGATGAGGAGAAAGATAATGCAAAGAGATGTTGAG ATAGAGGTTGAAACCGTTGATAGAACTGGAACGTTCTTGGGATCCTTATGG
genomic: ACGAAGCAATTGCTCTGATGAGGAGAAAGATAATGCAAAGAGATGTTGAGgtaaatcaat ... ttgtttgcagATAGAGGTTGAAACCGTTGATAGAACTGGAACGTTCTTGGGATCCTTATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaggttcctgtatgctgcttattttattgttaaatattttgtattgtttgcagATAGAGGTTGAAACCGTTGATAGAACTGGAACGTTCTTGGGATCCTTATGGGAGTCGAGGACCAATGTGGCAATTACACTGCTTGAAGCTGGTCTTGCAA
tgcttattttattgtt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatcaattcctttctgaactttaggttcctgtatgctgcttattttattgttaaatattttgtattgtttgcagATAGAGGTTGAAACCGTTGATAGAACTGGAACGTTCTTGGGATCCTTATGGGAGTCGAGGACCAATGTGGCAATTACACTGCTTGAAGCTGGTCTTGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG