Sequence
atgc intronic sequence ATGC exonic sequence...tgagattttttctgtaatttcatggaactcccttttgcttcttgaccaatggtttatttggttgaagacttgaattattcccatcttcttttatctgcagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTACAAGGATGAAGAGACGGCTTTGAGTGCTCGACGAAATCTTCAGGGT
Basic information
species | Glycine max |
transcript | GLYMA20G31220.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G31220.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g07490.1 (Oryza sativa), 3'ss of exon 2
tgagattttttct-gtaatttcatggaactcccttttgcttcttgaccaatggtttatttggtt-gaagacttg-aattattcccatcttcttttatctgcagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTACAAGGATGAAGAGACGGCTTTGAGTGCTCGACGAAATCTTCAGGGT
|| | ||| || | | | || | ||| | | || |||| | | || || ||| || | | || | | |||||| | |||||||| | |||||| ||||| ||||| |||||||| || ||||||||||||||||| ||||| ||| | ||||| || || || ||||| |||
tgccaagtttcctagcagctgca---agtgttttttaatctggtaacacgtggtaagatagtttcgactactcataagctcttaaacatttggtgctttgcagATTGGTTATTGATAAAGAAACAGGGAAGCCAAAGGGTTATGGGTTTTGTGAGTACAAGGATGAGGAGACTGCTCTAAGTGCACGCCGGAACCTTCAAGGT
upper sequence: GLYMA20G31220.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G096480_T03 (Zea mays), 3'ss of exon 2
tgagattttttctgtaatttcatggaactccct-tttgcttcttgaccaatggtttatttgg---ttgaa---gacttgaattattcccatcttctt-ttatctgcagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTACAAGGATGAAGAGACGGCTTTGAGTGCTCGACGAAATCTTCAGGGT
|| | | | | || || | | ||| || || || | || || | ||||| || || | | | | || | || || ||| | || ||||||| ||| || || || |||||||||||||| || || |||||||||||||| || || ||||| ||||| || || || |||||||||
------ttctggtttggtaacactgattaacatgtttactact--actgttaagtttttcagcatttgaatttgattttggtaactgactgctacaaattgcttgtagATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGATGAGGAAACTGCTTTAAGTGCACGCCGGAACCTTCAGGGT
upper sequence: GLYMA20G31220.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G174919_T03 (Zea mays), 3'ss of exon 1
tgagattttttctgtaatttcatggaactcccttttgcttcttgaccaatggtttatttggttgaagacttgaattattcccatcttctt-ttatctgcagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTACAAGGATGAAGAGACGGCTTTGAGTGCTCGACGAAATCTTCAGGGT
| | || ||| || || | ||| || | |||| || |||| | | || | | | || | || ||||| | || ||||||| ||| ||||| || |||||||||||||| || || ||||||||||| || || || ||| | ||||| || || || |||||||||
taacatgtttgctacggttatgtttttgcaacttgtgaat-ttgattaaaatgctattgagctatgctttttggcaactgactgctacaaattgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT
upper sequence: GLYMA20G31220.2 (Glycine max), 3'ss of exon 2
lower sequence: AT1G71800.1 (Arabidopsis thaliana), 3'ss of exon 2
-tgagattttttctgtaatttcatggaactcccttttgcttcttgaccaatggtttatttggttgaagacttgaattattccca----tcttcttttatctg---cagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTACAAGGATGAAGAGACGGCTTTGAGTGCTCGACGAAATCTTCAGGGT
| || ||| | | |||| ||| ||||| | || | || | | || | | | | || ||||| | |||| |||||| || ||||||||||| ||||||||||| || ||||| |||||||| || || ||||| || || || |||||||| || ||||||||| ||
gtcagttttatcgttcaatt--atgatttagggttttgataaaggaaacacttttcttcaaacaaacgaaacacagaagcctaaaaaactttgctttattggattcagATTAGTTACGGATAGAGAAACTGGTAAACCAAAAGGCTACGGATTTTGTGAGTATAAAGACGAAGAAACAGCATTAAGTGCTCGTCGTAATCTTCAGAGT
upper sequence: GLYMA20G31220.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g01800.t01 (Vitis vinifera), 3'ss of exon 2
--tgag-attttttctgtaatttcatggaactcccttttgcttcttgaccaatggtttatttggttgaagacttgaattattcccatcttcttttatctgcagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTACAAGGATGAAGAGACGGCTTTGAGTGCTCGACGAAATCTTCAGGGT
||| |||| || | || | | ||| ||||| | | | | |||| | | ||| | ||||| | || ||| || |||| | |||||||| ||||||| ||||| |||||||||||||||||||||||||| |||||||||||||| || || |||||||| || |||||||||||
aatgaacgttttctccacatttccct--cactttcttttagtaac-agcaatttgtttctatttcctttttctttatttatttatttatttattttgcttcagATTGGTTATTGATCGAGAAACAGGGAAGCCAAAAGGTTATGGATTCTGTGAGTATAAGGATGAAGAGACAGCATTAAGTGCTCGTCGTAATCTTCAGGGCMapped 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|4313812|gb|AI460931.1|AI460931EST: GAACAGCTTATCGAAATCTGCCAAGAGGTTGGCCCAGTAGTCTCATTCAG ACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGA
genomic: GAACAGCTTATCGAAATCTGCCAAGAGGTTGGCCCAGTAGTCTCATTCAGgtaactttta ... ttatctgcagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaatggtttatttggttgaagacttgaattattcccatcttcttttatctgcagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTACAAGGATGAAGAGACGGCTTTGAGTGCTCGACGAAATCTTCAGGGT
ttattcccatcttctt CT-rich tract
ttgaattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgagattttttctgtaatttcatggaactcccttttgcttcttgaccaatggtttatttggttgaagacttgaattattcccatcttcttttatctgcagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTACAAGGATGAAGAGACGGCTTTGAGTGCTCGACGAAATCTTCAGGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - -ttctgta
- - - - - - - - - - catggaa
- - - - - - - - - - - - - -ctccctt
- - - - - - - - - - - - - - - - - -tgcttct