Sequence
atgc intronic sequence ATGC exonic sequencegtagaattatgttcttgttcctggttgtttcctatgatataatgcattaatgcacctgttgtcttctcttttcagATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
Basic information
species | Glycine max |
transcript | GLYMA13G43680.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 6
-----------------gtagaatta--tgttcttgttcctggttgtttcctatgatataatgcattaatgcacctgttgtcttctct---tttcagATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
|| | || || | ||| || | | | || | | || | || || | | | |||||| | |||| |||||| || |||||||||||||| || || |||| ||| ||||| || |||||||||||||| ||||| |||||||| |||||
gtttgcgattttgttccttacatttgcttggcatagtttttgcatttctaacatttcttggtctggatttgaatgtggtgcccttatttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACT
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 7
--------------------------gtagaattatgttcttgttcctggttgtttcctatgatataatgcattaatgcacctgttgtcttctc-ttttcagATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
| || |||| | || || ||| | || || || | | | | || ||| ||| ||||||||| |||||| || |||||||||||||| || ||||||| |||| ||||| || |||||||||||||| || || ||||||||| |||||||
gtatacccatatgttttattttgttttaatgataatgtattaatttctcgttttcctctttgctagccttaacgagcaattttctttacttgaaatttctagATTTGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTGGATGGTCATTCAAAAGGTGTCAATTGTGTTGATTACTTCACTGGTGGTGACCGGCCATATC
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------gtagaattatgttcttgttcctggttgtttcctatgatataatgcattaatgcacctgttgtcttctcttttcagATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
|| ||| | || | || | | | | | | | | | | | ||||||||||||||||||| || || || || |||||||| |||||||| |||||||||||||| |||||||| |||||||| || |||||||| || || |||
gtgctgaaatggtctaacattgaaacatcattatggtttagtccgcttagtccgctcattctacgtttacatgcatgttcatcttcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 6
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 6
----------------------gtagaattatgttcttgttcctggttgtttcctatgatataatgcattaatgc-acctgttgtcttctctt---ttcagATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
| ||||| | ||| | | | | | | | | | | | | | | | | | ||||||| ||||||||||| || || || || |||||||| |||||||||||||||||||||| || ||||| |||||||| ||||| ||||| ||||| ||||
gtgtgtaagaggtccaagcactgagcttttatggcttagttagcacgaggtacttttaaaagggttttcttagactaattttcatgcttgttcatattcagATATGGAATCTTGGTTCCCCAGACCCAAATTTTACACTGGATGCTCATCAGAAAGGAGTCAACTGTGTAGATTATTTCACAGGGGGTGATAAACCCTATC
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 10
------------------------gtagaattatgttctt--gttcctggttgtttcctatgatataat--gcattaatgcacctgt-----tgtcttctcttttc-agATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
|| | | ||||| |||| || ||||| | | |||| | ||||| |||| |||| | |||| ||||||||||||||||| ||||| ||||||||||||||||| |||| ||||| || || ||||| || || ||||| ||||| || |||||||| |
gtaagattagtcttcaacttttaagttacaccttcttctttcattcccaatttcccattatgagaagcttaacatttgttttcctgtatctacatcttttcttacctagATATGGAATCTTGGCTCTCCGGATCCAAATTTTACTTTGGATGCACATCTCAAAGGGGTAAACTGTGTAGACTACTTTACTGGTGGGGATAAACCATACC
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------gtagaattatgttcttgttcctggtt-gtttcctatgatataa---tgc-attaatgcacctgttgtcttctcttttc-agATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
|| || | || || | || || | ||| | ||| | ||| ||| |||| | | | | |||||| |||| ||||||||||||||||| || ||||||||||| ||||||| ||||||||||| || |||||||||||||| |||||||| ||||| ||||||||||
gtatgatctggattttctgttggcaacttgtt-aactgcatttttttaccaattttgcttcatcaagtatgagtgtgctatttatgctctgatgatatctccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
----------------------gtagaatt----atgttcttgttcctggttgtttcctatgatataatgcattaatgcacctgttgtcttctcttttcagATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
| | || || || ||| || || | | | || | ||||| | || | || || |||||||||||||| ||||| ||||| || |||||||||||||||| || |||||| || || ||||||||||| || || ||||||||||| |||||
tatactttaagtcgctgttttggcggctttttcaatacagtttttctcctttacttataaaaaaaaaaagtcctaatgttgat-ctggcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S61_1V6.1 (Physcomitrella patens), 3'ss of exon 6
----------gtagaattatgttcttgttc--------ctggttgtttcctatga----tataatgcattaat---gcacctgttgtcttctcttttcagATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
| | | | ||| ||| | || | | ||| || || |||| ||||| | | | | ||| ||||| |||||||| || || || || || || || ||| | || |||||||||||||||||||||||||| || || |||| |||||||| ||| ||||
aagggacagtgccaactcaagttactgtccgctatgaactactcgcttcttacgaagcatatagtgcatgtttttgacgttaagcatgtattctgcacagATCTGGAATCTGGGTTCACCCGAACCCAACTTCACTCTAGAGGCTCATCAGAAAGGAGTGAATTGTGTCGAATACTTTAGTGGTGGTGATCGACCTTATCMapped 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|213613750|gb|DB961247.1|DB961247EST: CCAAAGACACAAACACCTTTGCTAGTGCATCTCTTGATCGGACAATAAAG ATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAG
genomic: CCAAAGACACAAACACCTTTGCTAGTGCATCTCTTGATCGGACAATAAAGgtagaattat ... ctcttttcagATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAG
EST:
gi|9987279|gb|BE661387.1|BE661387EST: AGTGCATCTCTTGATCGGACAATAAAG ATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAG
genomic: AGTGCATCTCTTGATCGGACAATAAAGgtagaattat ... ctcttttcagATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggttgtttcctatgatataatgcattaatgcacctgttgtcttctcttttcagATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
cattaat putative branch site (score: 3)
cacctgttgtcttctc CT-rich tract
atataatgcattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagaattatgttcttgttcctggttgtttcctatgatataatgcattaatgcacctgttgtcttctcttttcagATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG