Sequence
atgc intronic sequence ATGC exonic sequencegtaagacatcctcaagtttttgatttaggacaatttgatttgatgtgaataaaggtgtctgacatgtatccttttgcagGTTTGAAGATAAGGAAGTTCAACGAGACATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
Basic information
species | Glycine max |
transcript | GLYMA08G02960.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 2
---gtaagacatcctcaagtttttgat-ttaggacaatttgat--ttgatgtgaataaaggtgtctgacatgtatccttttgcagGTTTGAAGATAAGGAAGTTCAACGAGACATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
| || | | | | | | ||| | ||| | | || | || | || | | ||||||||||||||| ||||||||||| | |||||||| ||||| || || |||||||| |||||||| || || || ||||| ||||| || || ||||||||
gtaatggcactttaccctatgctcgctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttgcagGTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGATTGTGAACAAGGACGGTAAGCCCTACATTCAGGTCAAGATCAAGGATGGA
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 2
gtaagacatc-ctcaagtttttgatttaggacaatttgattt-gatgtgaataaa----ggtgtctgacatgta-------tccttttgc--agGTTTGAAGATAAGGAAGTTCAACGAGACATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
|||| || || ||| || || | ||||| | | | |||| | | || |||| | | || || ||| ||||| | || |||||||| || | |||||||| |||||||| || |||||| | ||||||||||| || || ||||| ||||| || || ||||||||
gtaacacctctctcctacagttacttctgttgaatttcgtctcgttgtgggttatttctggcgtcttaactttagtaatgccccatttatttagGTTCGCGGACAAGGAAGTCCAGAGGGACATGAAACTTGTTCCCTACAAGATTATTAACAAGGATGGCAAGCCCTACATTCAGGTCAAGATCAAGGATGGG
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 2
gtaagacatcctcaagtttttgatttaggacaatttgatttgatgtgaataaa----ggtgtctgacatgtat--ccttttgc--agGTTTGAAGATAAGGAAGTTCAACGAGACATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
||| | || | || | || | | | |||| | | || |||| || |||| || |||| |||||| | ||||||||||| || | |||||||| ||||| || || |||||| | ||||||||||| || || ||||| ||||| || || ||||||||
gtagtgcctctctcccacaattgcttctattatttcgtctcgctgtgggttatgtctggcgtcttacctgtaatgcccattgcttagGTTTCAGGATAAGGAAGTCCAGAGGGACATGAAACTTGTCCCCTACAAGATTATTAACAAGGATGGCAAGCCATACATTCAGGTCAAGATCAAGGATGGG
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 2
gtaagacatc-------ctcaagtttttgatttaggacaatttgatttgatgtgaataaaggtgt--ctgacatgtat-----ccttttgcagGTTTGAAGATAAGGAAGTTCAACGAGACATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
|||| || || || ||| ||||| | || | ||| ||| | || || || | | |||| | | | ||| |||||||||||||||||| ||||| ||||||||||||||||| || || ||||| ||||||||||| || |||||||| || || || || |||||||||
gtaatacgtctatctatctaaagcttttggtctatgc--attgtattagttggcaaggaactttttgctgaggcttttaatcacttttgacagGTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAACATTGTTAACAAGGATGGGAAGCCTTACATTCAAGTCAAGATCAAGGATGGT
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ17607 (Selaginella moellendorffii), 3'ss of exon 2
gtaagacatcctcaagtttttgatttaggacaatttgatttgatgtgaataaaggtgtctgacatgtatccttttgcagGTTTGAAGATAAGGAAGTTCAACGAGACATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
||||| | || ||| |||| | | ||| | ||| ||| || | | | |||||||||||| || || |||||| ||| |||||||| |||| | |||||| |||||||||||||||||||| ||||| || || || | ||||||||
gtaagttagattcccatttgcaatttttc-ctacttgttccttcttga---------tctaactctcgtaccgtcacagGTTTGAAGACAAAGAGGTTCAAAAAGATATGAAGCTCTTTCCATTTAAGATCGTCAACAAGGATGGAAAACCGTACATCCAAGTCAAGGTGAAGGATGGC
upper sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 2
gtaagacatcctcaagtttttgatttaggacaatttgatttgatgtgaataaaggtgtctgacatgtatccttttgcagGTTTGAAGATAAGGAAGTTCAACGAGACATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
| || || |||| | || | ||| ||| || | | | ||||||||||| || || |||||| |||| |||||||| |||| | |||||| |||||||||||||||||||| ||||| || || || | ||||||||
-------gtaagttagattcccatttgcaatttttccttccttcttga---------tctaactctcgtaccgtcatagGTTTGAAGACAAAGAGGTTCAAAGAGATATGAAGCTCTTTCCATTTAAGATCGTCAACAAGGATGGAAAACCATACATCCAAGTCAAGGTGAAGGATGGCMapped 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|120530199|gb|EH258333.1|EH258333EST: GTCAACCCAGAAAGGGTCATCTTTGATGTCAAGAGACTTATTGGAAGAAA GTTTGAAGATAAGGAAGTTCAACGAGACATGAAGCTTGTTCCTTATAAGAT
genomic: GTCAACCCAGAAAGGGTCATCTTTGATGTCAAGAGACTTATTGGAAGAAAgtaagacatc ... ccttttgcagGTTTGAAGATAAGGAAGTTCAACGAGACATGAAGCTTGTTCCTTATAAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaggacaatttgatttgatgtgaataaaggtgtctgacatgtatccttttgcagGTTTGAAGATAAGGAAGTTCAACGAGACATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
gtctgac putative branch site (score: 3)
tatcctttt putative PPT
aatttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagacatcctcaagtttttgatttaggacaatttgatttgatgtgaataaaggtgtctgacatgtatccttttgcagGTTTGAAGATAAGGAAGTTCAACGAGACATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG