Sequence
atgc intronic sequence ATGC exonic sequence...aattataacttttttaacatgtctacaatttatttttctatattttttcataagggtctaatgggtttcttctgttatgttttcttgcatttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA
Basic information
species | Glycine max |
transcript | GLYMA17G20610.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------------------------------aattataacttttttaacatgtctacaatttatttttctatatttt-ttcataagggtctaatgggtttcttctgttatgttttcttgcatttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA
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gtactcatatatttgaatttacatgcttgcgtcctgaatatggtgtcatggtgtctcagtctggtatattgatacatcatacatgtaccattttctccacttaagcaattgtactttcttcgcgaggcatcagtgcgattgctgactaaatatttgtttc--tcaacaa-agATTGCTGATGTGTGGTCGTGTGGAGTAACCCTCTACGTAATGCTGGTTGGTGCATATCCTTTTGAGGATCCAGATGAGCCTAAGAATTTCAGGAAGACAA
upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G066867_T01 (Zea mays), 3'ss of exon 5
----aattataacttttt-taacatgtctacaatttatttttctatattttttcataagggtctaatgggtttcttctgttatgttttcttgcatttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA
| | || | | | | | | | | |||| || | | | ||| || || | ||| | | | || | || | || ||||| ||||||||||||||||| | || |||||||| || || |||||||| |||||||| || |||| || ||| | || |||||||||
atacacgcacggtttgtagtcatgtatatgtatagcaggaaactatgttggcaagttggaaccctatg----tcagtcactaactcttcgt-tactgaaaacaagGTCGCTGATGTGTGGTCATGTGGAGTAACGCTGTACGTGATGCTGGTCGGTGCATATCCATTTGAGGACCCAGATGAGCCTAAGAATTTCAGGAAGACAA
upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 6
-aattataacttttttaacatgtctacaatttatttttctatattttttcataagggtctaatgggttt--cttctgttatgttttcttgcatttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA
|| | | | | | ||||| | | | | | | || ||| | || | | ||||| | || || || || ||| | || ||||||| || ||||||||||| ||||| |||||||| ||||| || || ||||||||||||||||||||| ||||||| |||||||| || || ||||
agttttttattctgcttgagtgtcttccagacacacag-tgtttcattatctaattattcaaagaatcaaatttctggtttgactt-ttacaaa-aatttcagATTGCAGACGTGTGGTCATGTGGGGTAACATTATATGTTATGCTTGTTGGTGCATATCCTTTTGAGGATCCTGATGAACCCAAGGACTTCCGAAAAACAA
upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 6
lower sequence: PP1S240_91V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------aattataacttttttaacatgtctac--aatttatttttctat----atttttt----cataagggtctaa----tgggtttcttctgttatgttttcttgcatttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA
| || ||| | || ||| | | | | | | |||| ||||||| ||| || || | | | | |||| | ||| | ||| || |||| ||||| ||||| |||||||| ||||| || |||||| ||||||| |||||||| ||||||||||| |||| |||| | | || |||| || |
gtatgctgctcagacgaggattcgtttttgtgaggtgattggatttctggtatctctgcggagctcagtgtactatcgaaattttttagggcatgtggcatcaagttatcagggaactgagatatgcctacttcttgtgaatcgcagATTGCCGATGTGTGGTCGTGTGGAGTGACCTTGTACGTGATGTTAGTGGGGGCATATCCGTTTGAGGATCCCGATGACCCAAGGAATTTCAGGAAAACCA
upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 6
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------------aattataactttttta-acatgtctacaatttatttttctatattttttcataagggtctaatgggtttcttctgttat----gttttcttgcatttaatat-tagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA
| || || | | | || | | |||| | | | || || | | || || | || | | |||| | |||| || |||||||||| ||||| || || || ||||| || |||||| | || |||||||||||||| ||||||||| | || |||| | | || |||| || |
gtaagtttttcggaagcgtgttggttttagtggaataaattggttcttggacaatgctattatcatgcggaactgaagctatttttggtgtcggtgaggttacaagtgcacggctctttgtcagctaaagaggctgatttgc-cgtgatatacagATTGCAGATGTGTGGTCTTGCGGTGTTACCTTGTACGTGATGTTGGTTGGAGCATATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCAMapped 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|17152867|gb|BM142800.1|BM142800EST: CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG CTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
genomic: CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtt ... ttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcataagggtctaatgggtttcttctgttatgttttcttgcatttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA
ttgcatttaatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattataacttttttaacatgtctacaatttatttttctatattttttcataagggtctaatgggtttcttctgttatgttttcttgcatttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA