Sequence
atgc intronic sequence ATGC exonic sequencegtaggattgtttactattttgtgtagtgaagacttttgcttgtcacagatttttcaagctaatttctgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
Basic information
species | Glycine max |
transcript | GLYMA18G49770.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 3
-----------gtaggattgtttactattt-tgtgtagtgaagacttttgcttgtcacagatttttcaagctaatttc--------tgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
|| ||| | | | ||| | || | || | | ||||| || | | | |||||| |||| || ||| |||| || ||||| || || || || || || || |||||||||||| | ||| | ||||| ||||| | ||||||||||||||||| ||||| |||||||
gcttccgcattacagatttggtaattttttatatgcattgtactgatatgcttcagttag-catccgaggataattttcttttgtttgatctttgaattagATCATATCTGGTGTTGAATATTGCCATAGAAACATGGTGGTTCATCGTGATCTTAAGCCAGAGAACCTTCTTTTGGACTCCAAATGCAATGTTAAGATTG
upper sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 3
------------------gtaggattgtttactattttgtgtagtgaa--gacttttgcttgtcacagatttttca-agctaatttctgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
|| | | || || | | | || ||| || | || || | | || | || || || | ||||||| || || ||||| ||||| || | || ||||||||||| ||||| | |||||||| || || ||||||||||| ||||| ||||| |||||||
gtatgtttttattttattttatcaacatgtaactttccaagcaaccattcgattttatattatatttgagagttaagaattagctacttggctttgatgtagATAATATCAGGAGTGGAATACTGCCATCGAAACATGGTGGTTCACAGAGACCTCAAGCCTGAAAACTTGCTTTTGGACTCTAAATGCAATGTAAAGATTG
upper sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 3
gtaggattgtttactattttgtgtagtgaagacttttg---cttgtcacag-atttttcaagctaatttctgattttgg-------------aagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
| |||||| || ||| || | |||| | | ||| || ||| | | | | || || || | ||||||| ||||| || |||||||| || | |||||||| || |||||||| ||||||||||||||||||| ||||| || | |||||| | |||||||
----gtttgttttctctttaccataaccagtgtgtttgtagcgtatcatgtcatctttgagtttgagtgttgtttgtgtttgactcatatccgaatagATAATATCTGGTGTAGAGTACTGCCATCGTAATATGGTTGTCCATAGAGACCTGAAGCCTGAGAATTTACTATTGGATTCGAGGTGTAATATTAAGATTG
upper sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------gtaggattgtttactattttgtgtagtgaagacttttg--cttgtcacagatttt--tcaagctaatttctgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
|| | | | || | ||| || || | || | |||| | | |||| | | | |||||||| ||||| ||||||||||| |||||||||||||| ||||| |||||| | || |||||||| || |||||||| |||||||| ||||| |||||||
gtagaaattattattttcctatgaaatttgtccccctttttccttcatctctctcaaccgagtcgatagaatgtttgtgaattaaccataaatttacatttggtcaattctttgcct---gaacagATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGATCTTAAACCTGAGAACTTGCTTTTGGATTCCAAATGCAATGTGAAGATTG
upper sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S7_365V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------gtaggattgtttactattttgtgtagtgaagacttttgcttgtcacagatttttcaagct--aatttctgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
| | ||| || | ||| ||||| || || ||||| ||| ||| || | |||| || || || |||||| | ||||| ||||| || || || |||||||||| |||||| | || |||||||| ||||| |||||| | ||||||||||| || |||||||| |
aggtaaattccttggttgtttgaatggaatttttgaggattctgtgtggtc----ctcttgctcttcaggcttttatctggtataaattgctcatgctgc--gcagATTGTGTCTGGCGTGGAATATTGCCATCGGAATATGGTTGTTCATCGTGACTTGAAGCCAGAGAACTTACTTCTCGACTCCAAATGGAACGTCAAGATAG
upper sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ35371 (Selaginella moellendorffii), 3'ss of exon 2
gtaggattgtttactattttgtgtagtgaagacttttgcttgtcacagatttttcaagctaatttctgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
|| | | || || || ||| | || ||| | | | ||||| || ||||| ||||| || |||||||| ||||||||||||||| | ||| ||||||| || ||| | | | ||||| | || ||||| |||||||
----------------------gtt-cgtgctccttcgcctggtgaagaaaactgaatataactc--gcacacatcaccagATCATTTCTGGAGTGGAATATTGTCACAGAAATATGGTGGTTCATCGTGATCTGAAGCCAGAAAATCTGTTGCTTGACTCTAGGTGCAATGTGAAGATTGMapped 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|254315447|gb|GR825256.1|GR825256EST: TAGAGAAGGGTAGGTTGCAGGAAGATGAAGCTCGTAANNNNNNNCAGCAG ATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGAT
genomic: TAGAGAAGGGTAGGTTGCAGGAAGATGAAGCTCGTAATTTTTTTCAGCAGgtaggattgt ... ttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGAT
EST:
gi|254336679|gb|GR842858.1|GR842858EST: TAGAGAAGGGTAGGTTGCAGGAAGATGAAGCTCGTAANNNNNNNCAGCAG ATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGAT
genomic: TAGAGAAGGGTAGGTTGCAGGAAGATGAAGCTCGTAATTTTTTTCAGCAGgtaggattgt ... ttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaagacttttgcttgtcacagatttttcaagctaatttctgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
ttctgat putative branch site (score: 3)
taatttctgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggattgtttactattttgtgtagtgaagacttttgcttgtcacagatttttcaagctaatttctgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC