Sequence
atgc intronic sequence ATGC exonic sequence...tgtatgaagttatgaacatatttgcttgatttatgctgtctaagaatttaaatattatcgatttatgccttagaaattttctgattctatgaacttgcagGAAGTGTTCATGATGCATGATGATGCTGTGCTTTGTGTAGACTTTAGCAGAGATTCAGAAATGCTTGCATCTGGGTCTCAAGATGGAAAGATTAAA
Basic information
species | Glycine max |
transcript | GLYMA08G13560.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 7
-----------------------------------------------------------------------tgtatgaagttatgaacatatttgc-ttgatttatgctgtctaagaatttaaatattatcgatttatgcct---tagaaattttc-tgattct-----atgaacttgcagGAAGTGTTCATGATGCATGATGATGCTGTGCTTTGTGTAGACTTTAGCAGAGATTCAGAAATGCTTGCATCTGGGTCTCAAGATGGAAAGATTAAA
|| ||| | | ||||| || || | | | || | || || | ||| | | || |||||| | ||| | | | || |||||| ||||||||||| |||||||| ||||||| ||| || || || |||||||| || ||||| |||||||| || || ||||||||||||||
gtaaggccataggattgatgttttctcaaattgaacaacgaattaagttattaacacgattactgtactggtgcatgtggaaagcaacatcttcaagttcagcagctttatggggacatgcatatgttcttttttttagtttaaatataaatttcaataattttcaaaaaccactttacagGAAAGCTTCATGATGCACGATGATGCGGTGCTTTCTGTTGATTTCAGTAGAGATTCTGAGATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG
upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 7
tgtatgaagttatgaacatatttgcttgatttatgctgtctaagaatttaaatattatcgatt----tatgccttaga----aattttctg----------attctatgaac-ttgcagGAAGTGTTCATGATGCATGATGATGCTGTGCTTTGTGTAGACTTTAGCAGAGATTCAGAAATGCTTGCATCTGGGTCTCAAGATGGAAAGATTAAA
||||| | | | | | |||| ||| || |||| || | || ||| | | ||| || || |||||| | | |||||| | |||||| || |||||||| || || ||||||| ||||| || ||||| || ||||| |||||||| |||||||| || || ||||||||||||||
-gtatgtgcctttaagttttgtagctttatt-ataggacttaagtatgcacattctatttaatcagacatggctaaggtgctaattttttatgtactgtctgctggatgaacacttcagGAAAGCTTTATGATGCACGAGGAACCTGTGCTGTGTGTTGATTTTAGTAGGGATTCTGAAATGCTGGCATCTGGATCACAGGATGGAAAGATTAAG
upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 8
lower sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 8
---tgtatgaagttatgaacatatttgcttgatttatgctgtctaagaatttaaatattatcgatttatgccttagaaattttctgattctatgaacttgcagGAAGTGTTCATGATGCATGATGATGCTGTGCTTTGTGTAGACTTTAGCAGAGATTCAGAAATGCTTGCATCTGGGTCTCAAGATGGAAAGATTAAA
|||| || || | | | | || | | || || || | | || | | | | | ||||| | || |||||| |||||||||||||||||| |||| || || |||||||||||||||||||||| ||||||||||||||||| ||||||||||||||||||
ccaagtatctcgtctgagacttcctggtatacaaaatatcagttttggata-aagagttcccattccatcctctttacttactatgattaattt--ctgacagGAATCTTTCATGATGCATGATGATCCTGTCCTCTGCATAGACTTTAGCAGAGATTCAGAGATGCTTGCATCTGGGTCACAAGATGGAAAGATTAAA
upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 8
tgtatgaagttatgaacatatttgcttgatttatgctgtctaagaatttaaatattatcgatttatgccttagaaattttctga--ttctatgaactt--gcagGAAGTGTTCATGATGCATGATGATGCTGTGCTTTGTGTAGACTTTAGCAGAGATTCAGAAATGCTTGCATCTGGGTCTCAAGATGGAAAGATTAAA
| || | | || | | || | || |||||| | || | | || ||||| |||| | |||||||||| |||||| || |||||||||||||||||||| |||||||| || |||||||||||||| || |||||||||||||| || ||||||||||| || |||
---cctatttttggttcctacaaagcacaaagaaact-tttagcaatttatctttttggcagaggcctcctatgaatttgctgacatgctatgaacttttacagGAAACCTTTATGATGCATGATGATGCTGTCCTTTGTGTTGATTTTAGCAGAGATTCGGAGATGCTTGCATCTGGATCACAAGATGGAAAAATCAAAMapped 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|193465598|gb|FK432503.1|FK432503EST: GGGATTACATAAGTGGAAAGCTGAAGAAAGATCTACAGTACCAGGCTGAT GAAGTGTTCATGATGCATGATGATGCTGTGCTTTGTGTAGACTTTAGCAGA
genomic: GGGATTACATAAGTGGAAAGCTGAAGAAAGATCTACAGTACCAGGCTGATgtgagtgagt ... gaacttgcagGAAGTGTTCATGATGCATGATGATGCTGTGCTTTGTGTAGACTTTAGCAGA
EST:
gi|192300449|gb|FG987906.1|FG987906EST: GGGATTACATAAGTGGAAAGCTGAAGAAAGATCTACAGTACCAGGCTGAT GAAGTGTTCATGATGCATGATGATGCTGTGCTCTGTGTAGACTTTAGCAGA
genomic: GGGATTACATAAGTGGAAAGCTGAAGAAAGATCTACAGTACCAGGCTGATgtgagtgagt ... gaacttgcagGAAGTGTTCATGATGCATGATGATGCTGTGCTTTGTGTAGACTTTAGCAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttaaatattatcgatttatgccttagaaattttctgattctatgaacttgcagGAAGTGTTCATGATGCATGATGATGCTGTGCTTTGTGTAGACTTTAGCAGAGATTCAGAAATGCTTGCATCTGGGTCTCAAGATGGAAAGATTAAA
ttctgat putative branch site (score: 3)
aatattatcgatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtatgaagttatgaacatatttgcttgatttatgctgtctaagaatttaaatattatcgatttatgccttagaaattttctgattctatgaacttgcagGAAGTGTTCATGATGCATGATGATGCTGTGCTTTGTGTAGACTTTAGCAGAGATTCAGAAATGCTTGCATCTGGGTCTCAAGATGGAAAGATTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
tgtatga
- - - - - tatgaac
- - - - - - - - - - - tgcttga
- - - - - - - - - - - - - - - - -tgctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcct