Sequence
atgc intronic sequence ATGC exonic sequence...aagcatagaatcatgatattccaaatgcatattttagcttagttttatgaagttgctgtcattctcatttcattttgtgttgctttatcatgttttcaggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGG
Basic information
species | Glycine max |
transcript | GLYMA18G08180.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 5
aagcatagaatcatgatattccaaatgcatattttagcttagttttatgaagttgctgtcattctcatttc----attttgtgttgctttatcatgttttcaggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGG
| || | |||| | | | | || || || || | | || | | || |||| | | | ||| | | | |||||| || ||||||||||| || ||||| ||||| || || |||||||||||| ||||||| ||||| |||||||| |||||||| |||||||||||||
gaaaattggatcac--tgattacagtttattcttctctttgtttatccatatctgttttactttatgtttcagagaaaccctaatattttgactt-ctgtcagGTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAG-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 5
--aagcatagaatcatgatattccaaatgcatattttagcttagttttatgaagttgctgtcattctcatttcatt--ttgtgttgctttatcatgttttcaggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGG
| || |||| | | | | | || | ||| || | | ||| | | || ||||| | | ||| | || | |||||| || ||||||||||| || ||||| ||||| || || |||||||||||| ||||||| ||||| |||||||| ||||||||||||||||| ||||
aagaaaattagatcac--tgcttatagtttgttcttcactttatttattcatatttgttttactttatgtttcagagaccctaatattttgac-tgctgtcagGTCAATCCTTCAGATGTAATTATTTTGGAAGGTATTCTGGTTTTCCATGATTCACGTGTCCGGGACTTGATGAACATGAAGATATTTGTTGATACAG-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 5
aagcatagaatcatgatattccaaatgcatattttagct-tagttttatgaagttgctgtcattctcatttcattttgtgttgctttatcatgttttcaggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGG
| || | || | ||| | | ||| | | | || || || | | || | | || | ||| ||||| || |||||||||||||| ||||| ||||| || || ||||| |||||| |||| | |||| |||||||| |||||||| || ||||| ||||
taacagaaaacatttgctttctgctggtttgtttacgttatttattcatcaatgcaatacttgatttatacaagcaaccctaatttaaaactgtcgccagGTTAATCCTTCAGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATCTTCGTTGATACAG-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 6
------------------------------------------------------------------------aagcatagaatcatgatattccaaatgcatattttagct-tagttttatgaagttgctgtcattctcatttcattttgtgttgctttatcatgttttcaggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGG
| || | || | ||| | | ||| | | | || || || | | || | | || | ||| ||||| || |||||||||||||| ||||| ||||| || || ||||| |||||| |||| | |||| |||||||| |||||||| || ||||| ||||
gtaagtacctgatacactatttgctatttgtacaaccgcttatttcttcacatcgatttcgtattgtacatttaacagaaaacatttgctttctgctggtttgtttacgttatttattcatcaatgcaatacttgatttatacaagcaaccctaatttaaaactgtcgccagGTTAATCCTTCAGATGTTATTATTTTGGAAGGAATTCTAGTTTTTCATGATTCACGCCTCAGGGATTTGATGAACATGAAGATCTTCGTTGATACAG-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 5
aagcatagaatcatgatattccaaatgcatattttagcttagttttatgaagttgctgtcattctcatttcattttgtgttgctttat--catgttttcaggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGG
||| | || || | | || || |||| | | | | | |||| || || | | | | | ||||| || ||| |||||||| ||||| || ||||||||| | ||||| || || |||||||||| || || || || || |||||||| |||||||||||||| ||| |||
ttacatgcactcttg-tttgtcagatacataaacttgtcatcatagcctatataagaatcatgcttatactaatatttctctgtttatgatatatttgcagGTGAATCCTTCTGACGTTATAATTCTGGAAGGTATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 5
aagcatagaatcatgatattccaaatgcatattttagcttagttttatgaagttgctg--tcattctcatttcattttgtgttgctttatcatgtttt-caggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGG
|| | ||| | | ||| | | |||| | | | | ||| |||| || | | | | | | || | ||||| || ||| ||||||| |||||| | ||||| || ||| | |||||||||||||| || || |||||||||| |||||||| |||||| |||||
aatttcttag--atgtcaccactggcttttatctggttggggatttaaggggagatcaatttaatcttatttgatgctaggattttgaaaaacattctgcagGTAAATCCTACAGATGTAATAATTCTTGAAGGGATACTTTTGTTCCATGATCCACGCGTCCGAAAGTTGATGAACATGAAGATTTTTGTTTGCACAG-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 5
aagcatagaatcatgatattccaaatgcatattttagct--tagttttatgaagttgctgtcattctcatttc-attttgtgttgctttatcatgtttt-caggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGG
|| | | | || | | |||||| || | | | ||| || | || | |||| | ||||| | || ||| ||||| |||||||||||||| |||||||| |||||||| || |||| ||||||| ||||| ||||| |||||||| ||||||||||||||||| ||||
-agggtggt-cctgaatcctgtgagattatatttcaggtacttgatttctgttcccgg-gttacatgcattgagaaccctcattgctatgaaatatttggcagGTCAACCCTTCAGATGTGATAATTTTGGAAGGCATACTCATTTTTCATGATCTTCGTGTCCGGGAATTGATGAACATGAAGATATTTGTTGATACAG-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S83_234V6.2 (Physcomitrella patens), 3'ss of exon 5
-----------------aagc-atagaatcatgatattccaaatgcatattttagcttagtt--ttatgaagttgctgtcattctcatttcattttgtgttgcttta---tcatgtt----ttcaggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGG
| || |||| | || ||| | | || || ||| | | || ||| || |||| | || || | | ||||| || | || ||||| || ||| | || || || | | || |||||| | ||||||||||||| |||||||||||||| |||||||| ||||
gtgattctttaagtaccatgctgccagttcattagtttgtggatgtttgctcatttttggtcgacgatgcgtgaataattaagagcaaaccataccatgctgctaaaagttcctggtcacctgcagGTCAATGCATCTGATGTAATTATTGTGGAGGGAATATTGATCTTTCATGATGCTCGTGTTCGGGAGTACATGAATATGAAGATCTTTGTTGATACAG-Mapped 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|192329234|gb|FK020153.1|FK020153EST: TCCAAAGTATGATTTTAAGAGTTACAAGAGTGATGACATGTTAAGAAGGG TGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATC
genomic: TCCAAAGTATGATTTTAAGAGTTACAAGAGTGATGACATGTTAAGAAGGGtacgtctcag ... tgttttcaggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgaagttgctgtcattctcatttcattttgtgttgctttatcatgttttcaggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGG
tgttttc CT-rich tract
atttcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagcatagaatcatgatattccaaatgcatattttagcttagttttatgaagttgctgtcattctcatttcattttgtgttgctttatcatgttttcaggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - -catgata
- - - - - - - - - - - - -tgcatat
- - - - - - - - - - - - - - - - - - - - - - -tatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct