Sequence
atgc intronic sequence ATGC exonic sequence...tcatttgcttctgtatccagaaaattattactaaatatttgagcaaatgtgtattgtgaacctttccatgttacctgaatgctttagttttgaattgcagGCCTTGGATTACTGCCATTCTCAAGGCATCATGCATAGGGATGTCAAGCCTCATAATGTTATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
Basic information
species | Glycine max |
transcript | GLYMA01G39950.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 3
--tcatttgcttctgtatccagaaaattattactaaatatttgagcaaatgtgtattgtgaacctttccatgttacctgaatgctttagt-tttgaattgcagGCCTTGGATTACTGCCATTCTCAAGGCATCATGCATAGGGATGTCAAGCCTCATAATGTTATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
||| ||| ||| | | | | | || | | | | | | | | || | || || ||| | | | || || ||||| ||||||||||| ||||||||||| || ||||| | |||||||||||||| ||||||||||| || ||||| | || || |||||||| || ||||
attcagttgggcttgt--tcggtgttcgtcgatttagtagccagg-acttatttctaatctcctgttatcttttttctaaattccgtcctgcttaccttccagGCATTGGATTACTGTCATTCTCAAGGAATTATGCACCGCGATGTCAAGCCTCACAATGTTATGATTGACCATGAACTCCGCAAGCTTCGCTTAATTGATT
upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 3
tcatttgcttctgtatccagaaa-attattactaaatatttgagcaaatgtgtattgtgaacctttccatgttacctgaatgcttta-gttttgaat-tgcagGCCTTGGATTACTGCCATTCTCAAGGCATCATGCATAGGGATGTCAAGCCTCATAATGTTATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
| || | | || | || || | | | || ||| ||| |||| |||| | || ||| | || || ||| | ||||||| || |||||||| ||||| ||||| || ||||| || |||||||||||||| |||||||||||||| |||||||| ||||||||| | |||| ||||
---tatgaaacaaactggaggctcagcatcacagagaacatctcaaattgttgcaagtgcttcttttcatgcttgcttaattcagtaagtcttgcgtatgcagGCATTAGATTACTGTCATTCACAAGGAATAATGCACAGAGATGTCAAGCCTCACAATGTTATGATAGACCATGAGTTGCGAAAACTTAGACTGATTGATT
upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 3
tcatttgcttctgtatccagaaaattattactaaatat-ttgagcaaatgtgtattgtgaacctttccatgtta--cctgaatgctttagttttgaattgcagGCCTTGGATTACTGCCATTCTCAAGGCATCATGCATAGGGATGTCAAGCCTCATAATGTTATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
| || || | || ||| |||| | | |||| | | || | ||| | | | ||| | | || |||| ||||||| ||||| || |||||||||||||| ||||| || |||||||| |||||||| ||||| ||||||||||| ||||||||| | || |||||||||||||||||||
-taattctttaaattggcaacaaactattggttcctgccttgaactcagcagtcctctgatagactactttttaaacttatctgattta--tttgaatatcagGCATTAGATTACTGCCATTCACAAGGTATAATGCATAGAGATGTCAAACCTCACAATGTTATGATTGATCATGAGCTTCGCAAACTTCGCTTGATAGATT
upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 3'ss of exon 4
-tcatttgcttctgtatccagaaaattattactaaatatttgagcaaatgtgtattg-tgaacctttccatgttacctgaatgctttagttttgaattgcagGCCTTGGATTACTGCCATTCTCAAGGCATCATGCATAGGGATGTCAAGCCTCATAATGTTATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
| | | || | |||| | || || | ||| || | | | ||| ||| || || | | || | ||| | ||||||| ||||| ||||||||||||||||| |||||||| |||||||| ||||| || ||||| ||||| || || ||| |||||| || | |||| ||||
ccccaccaccgcca-ataaaaaaaacgaatagaaaggaaatgaagttcggttttctactttacccttcaattttggattattgatg-gctttatcactgcagGCTTTGGACTACTGCCATTCTCAAGGGATCATGCACAGGGATGTGAAGCCACACAATGTAATGATTGACCACGAGCAACGAAAGCTGAGACTGATTGATT
upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 3
-tcatttgcttctgtatccagaaaattattactaaatatttgagcaaatgtgtattgtgaacct-ttccatgttacctgaatgctttagttttgaattgcagGCCTTGGATTACTGCCATTCTCAAGGCATCATGCATAGGGATGTCAAGCCTCATAATGTTATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
| || | | | | |||| || | ||| || || | | ||||| | | || | ||| | || | | || ||||||||||| ||||| ||||| ||||| || ||||| | || ||||| || |||||||| ||||| |||||||| |||||| | | || |||||||
attatg-ataacaacaacaataaaactaattgtaacaatcatagtatgag-gtattttcattgggttattcatcgattgagtactggcttgctctgtttcagGCCTTGGACTACTGTCATTCGCAAGGGATAATGCACCGAGACGTCAAACCACATAATGTGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATT
upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 4
---tcatttgcttctgtatccagaaaattattactaaatatttgagcaaatgtgtattgtgaacctttccatgttacctgaatgctttagttttgaattgcagGCCTTGGATTACTGCCATTCTCAAGGCATCATGCATAGGGATGTCAAGCCTCATAATGTTATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
| | | |||| | ||| |||| | || || || | | | | |||| | | || ||| | |||||||| ||||| || |||||||||||||| || ||||| |||||||| ||||| || || || ||||| || |||||| || || ||| | | || || |
ttttaaaattcttcctatcttggtttgccattcctaacaacttattatcatactcat-gcagagatataaatgtgggtt-actgacggagtcattg-ttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCACACAACGTGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACT
upper sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------------------------------------------tcatttgcttctgtatccagaaaattattactaa---atatttgagcaaatgtgtattgtgaacct--ttccatgttacctgaatgctttagttttgaattg---cagGCCTTGGATTACTGCCATTCTCAAGGCATCATGCATAGGGATGTCAAGCCTCATAATGTTATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
| | ||| | | | | | || | | | | || || |||||| | || ||| | || | | | | |||| || ||||||||||||||||| ||||| ||||| || |||||| | || ||||| || |||||||| ||||| ||||||||| |||||| | | | || ||||
gtaggttctacctaaactttgctcggcttgcattcaatcattacacttaattttcagtgttctatttatctgaattttagttgtgtatctgcttaaagaaacgtgcttgatgcgccgcagggctaagaaaaattgtggcattggctcaatgcttgatgta-gtcgtggctttgccctgtttcagGCCTTGGATTACTGTCATTCGCAAGGGATAATGCATCGAGACGTCAAACCACATAATGTGATGATTGATCATGAGCAGCGAAAATTAAGGCTCATCGATTMapped 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|213608123|gb|DB972591.1|DB972591EST: CAACCTTGACTGATTATGACATACGCTATTACATATATGAGCTCCTTAAG GCCTTGGATTACTGCCATTCTCAAGGCATCATGCATAGGGATGTCAAGCCT
genomic: CAACCTTGACTGATTATGACATACGCTATTACATATATGAGCTCCTTAAGgtagtatgat ... tgaattgcagGCCTTGGATTACTGCCATTCTCAAGGCATCATGCATAGGGATGTCAAGCCT
EST:
gi|213617929|gb|DB957382.1|DB957382EST: CNACCTTGACTGATTATGACATACGCTATTACATATATGAGCTCCTTAAG GNCCTTGGAT-ACTGCCATTCTCAAGGCATCATGCATAG
genomic: CAACCTTGACTGATTATGACATACGCTATTACATATATGAGCTCCTTAAGgtagtatgat ... tgaattgcagG-CCTTGGATTACTGCCATTCTCAAGGCATCATGCATAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgtgtattgtgaacctttccatgttacctgaatgctttagttttgaattgcagGCCTTGGATTACTGCCATTCTCAAGGCATCATGCATAGGGATGTCAAGCCTCATAATGTTATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
tttagttttgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatttgcttctgtatccagaaaattattactaaatatttgagcaaatgtgtattgtgaacctttccatgttacctgaatgctttagttttgaattgcagGCCTTGGATTACTGCCATTCTCAAGGCATCATGCATAGGGATGTCAAGCCTCATAATGTTATGATAGATCATGAGTTACGAAAACTTCGCTTGATAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - -tgcttct
- - - - - - - - ccagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgct