Sequence
atgc intronic sequence ATGC exonic sequencegtaaatttggacactaagatcttgctttggagcccttccttagagatattctagttctgggttactatcttcctgtaaattatatttgatatgaattatttctttttagATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATC
Basic information
species | Glycine max |
transcript | GLYMA07G00230.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 10
-------------------------------------------------gtaaatttggacactaagatcttgctttggagcccttccttagagatattctagttct----gggttactatcttcctgtaaattatatttgatatgaattatttctttttagATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATC
| | ||| || || || || | || | | ||| | ||| | | || || || | || ||| | ||| | | | | | | || |||| ||||||||||||||||||||| | ||||| || |||||||| || || ||||| || || || ||||| || |||||||| ||||| || |||||||
gtaatgttctatgtttgctgagtttttctaaatttaaatgcgttgttttgccaggctggtca-tactatttttgtatgcaactctttgggggggattctgccttcctccttaggctagcgtttttctgca--ctatctaatgctaggtctctatgtgttcagATAGGATATCTTGAATATTGCAAGCAGCGTGGATTCACAAGCTGTTACATATGGGCGTGCCCACCTTTAAAAGGTGAAGATTACATTTTGTACTGCCATC
upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 9
------------------------------------gtaaatttgg-acactaagatcttgctttggagcccttccttagagatattctagttctgggttactatcttc--ctgtaaattatatttgatatgaattatttctttt-----tagATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATC
|||||| | || | || | | || | || | | | | | | || || | || | ||| | | | | || || |||| |||||||||||||| || || || || || ||||| || || || ||||||||||| || || ||||| |||||||| || |||||||||||||
gtaatttgccatccatgctgactttttgtgactaatacaaatttattgccttaccaggtttggccaaaactgtttgg-ggggaccatatgactggaaactgttttttttagctaggatttgttcttggtctaatctgttctcattgtgtacagATAGGATATCTTGAATACTGTAAACTGCGGGGATTCACAAGTTGTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaaatttggacactaagatcttgctttggagcccttccttagagatattctagttctgggttactatcttc-ctgtaaattatatttga---tatgaattatttcttttta--gATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATC
|||| | | | || | |||| | || |||| | | | ||||| ||| | ||||| || | | ||| | | | ||||||| ||| || || || ||||| |||||| |||||||| || |||||||| || ||||||||||| || | ||||| || |||||||| |||||||| ||||
gtaagtcctggtcttctga---aaccttggtgtttaacc-----aatatctgtgcttt---ttactttctacactgtatggaggatctaagagtataatctgatcctttttatagATCGGCTACCTAGAATACTGCAAGTTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCGCCGCTGAAGGGCGAGGATTATATCTTATATTGTCATC
upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaaatttggacactaagatcttgctttggagcccttccttagagatattctagttctgggttactatcttcct--gtaaattatatttgatatgaattatttctttt-tagATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATC
| | || ||| | || | || || || | || || || | ||| ||| | || || ||||||| || ||||| || || ||||||||||| ||| ||||||||||||| ||||| || || || | ||||| |||||||||||||||||||||||||
------------------------gtaagccgcatttcttctgatcctagttgctttcaggcacctgtgttgcttcacaagtcttatcaacaatgggcttttcggattgcagATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAAGCTGCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATC
upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G55970.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaaatttggacactaag--atcttgctttggagcccttccttagagatattctagttctgggttactatcttcctgtaaattatatttgatatgaattatttctttttagATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATC
|||| | || | | ||| || | ||| ||| || | || | | | || || |||| ||| || ||||| | ||||||| ||||| || ||||| ||||||||||||||||||||||||||||| ||||| ||||||||| | ||||| || ||||| ||| | || || ||||
-------------gtaagccgttttatctctaatcccatcttctttaggtttcgtgttttgcttcacgag-tacatgaaacttatcattgttacgaatt-------tgcagATTGGTTATCTCGATTATTGTAAGAAACGTGGTTTTACAAGCTGCTATATATGGGCATGTCCTCCACTTAAGGGTGACGATTACATTCTTTACTGTCATC
upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaaatttggacactaagatcttgctttggagcccttcctta-gagatattctagttctgggttactatcttcctgtaaattatatttgatatgaattatttctttttagATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATC
|||| ||| | ||| | || ||| | | | ||||| | | || || | |||||| | || |||| ||||||| ||||| ||||| ||||| |||||||| || |||||||| || ||||||||||| ||| | ||||| || |||||||| ||||||||||||
-------------gtaagttctggtttttcaacctaggtttatgtggtcttctacattacatggatgat--tcaagggtattataccc--------tgatgctttttcagATTGGTTATCTGGAATACTGCAAATTGCGTGGTTTCACGAGCTGCTACATATGGGCTTGTCCACCACTGAAGGGTGAGGATTATATCCTATATTGCCATC
upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 9
gtaaatttggacactaagatcttgctttgga-gcccttccttagagatattctagttctgggttactatcttcctgtaaattatatttgatatgaattatt-tctttttagATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATC
|| | ||| | || | | ||| ||| | || || | | | ||| | | | | || | | | |||| ||| ||||| ||||||||||||| ||||| || ||||| || ||||| ||||| |||||||| |||||||||||||| || ||||| ||||| ||||| || ||||||||||
gtgagttttagtattacgccaatcttttatttattcttgatgagcaattcttatggtttggaatctttttatattg-ggctattggcttatatatccgattctctttccagATTGGATATCTCGAATACTGTAAGAAGCGGGGTTTCACAAGTTGCTATATATGGGCTTGTCCTCCTTTGAAGGGTGAAGACTATATATTGTATTGCCATC
upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S193_70V6.1 (Physcomitrella patens), 3'ss of exon 11
gtaaatttggacactaagatcttgctttggagcccttccttagagatatt-ctagttctgggttactatcttcctgtaaattatatttgatatgaattatttctttttagATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATC
||||| ||| || || | || ||| | | | | || | ||| | || | | ||| |||| | || || || | | ||||||| ||| | || ||||| || | ||||||| || || || || |||||||| || ||||||||||| || ||||||||||||||||| ||||
----atttg--tgttaatattttctgtaatagaactttggttctgctgctgctgctactgttcttctgtttgcct----attaaacttaattgtgtacatacttctgcagATTGGCTATTTAGACTATTGTCGGAGGAGAGGTTTTAGTAGTTGTTACATTTGGGCTTGCCCACCATTAAAGGGTGAGGATTATATTTTATATTGTCATCMapped 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|208268986|gb|GE069827.1|GE069827EST: AAGCAATGACGGGAGAGGCTCTTCGGACTTTTGTTTACCATGAAATTCTG ATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATC
genomic: AAGCAGTGACGGGAGAGGCTCTTCGGACTTTTGTTTACCATGAAATTCTGgtaaatttgg ... ttctttttagATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgggttactatcttcctgtaaattatatttgatatgaattatttctttttagATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATC
atttgat putative branch site (score: 5)
ttatttcttttt putative PPT
tgtaaattatatttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatttggacactaagatcttgctttggagcccttccttagagatattctagttctgggttactatcttcctgtaaattatatttgatatgaattatttctttttagATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA