Sequence
atgc intronic sequence ATGC exonic sequence...tatttagtttgcctgcatttatatgtctgtagaatgttatatgcaccataccaaatattcttttttatttatttatgtgatttaatttcatcctggatagGATAAGTCTTGGCGCGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
Basic information
species | Glycine max |
transcript | GLYMA10G42250.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------tatttagtttgcctgcatttatatgtctgtagaatgttat-atgcaccataccaaatat----tcttttttatt-tatttatgtgat---ttaatttc----atcc--tggatagGATAAGTCTTGGCGCGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
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gtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatattta-tttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG
upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------------------------------------------------tatttagtttgcctgcatttatatgtctgtagaatgttatatgc-accataccaaatattcttttttatttatttatgtgatttaatttcatcctggatagGATAAGTCTTGGCGCGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
| | | | | | || |||| || | | | ||||||| | ||| | || |||||| ||| | |||| ||||||| |||||||| ||||| || ||||| ||||||||| ||||||| || ||||||||||| || ||||||| || ||
gtatatcttacacacttttggtggcttaataaatgttgggagaaaagataaagttgtcaatactaattctcgtaaaaattactagagtaagatttccataagatctgctactagacaataatttcatgtgcttaagtttcagcacactaccatacatggttaatgatttcaattgcttatgt--tttcttaacatctc----agGATAAATCTTGGCGTGTGCGCTATATGGTGGCAAATCAACTGTATGAACTATGTGAAGCTGTTGGTACTGAACCCACAAG
upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 4
---------tatttagtttgcctgcatttatatgtctgtagaatgttatatgca--ccataccaaatattcttttttatttatttatgtgatttaatttcatcctgga-tagGATAAGTCTTGGCGCGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
| | | | | | || || || |||| | | | || | || | | | ||||| | || |||| || | || |||||||||| ||||| |||||||| |||||||||||||| | ||||| ||||||||||||||||| || || || || ||
gtaaataaatgtgtgaatatgataaaaaaattctattgatgagctttatgggaaagctgtaaggcagatatgtatgagctgctttatcttgatttttttcgtctttgagcagGATAAGTCCTGGCGTGTGCGTTATATGGTTGCAAATCAGCTCTATGAACTTTGTGAAGCTGTAGGACCGGAGCCAACTAG
upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 3
tatttagtttgcctgcatttatatgtctgtagaatgttatatgcaccataccaaatattcttttttatttatttatgtgatttaatttcatcctggatagGATAAGTCTTGGCGCGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
| ||||||||||| | |||| | || | | || | | | ||| | || ||| ||| |||||||||||||||| ||||| || ||||||||||||||| | || |||||||||||||| || || ||||| ||||| ||
----------------gtgattatgtctgtaggcttttatgctgatgat-ctacat---ttaaaagaaatgcttaatctttgtactttttcactgagcagGATAAGTCTTGGCGTGTGCGCTATATGGTTGCAAATCAACTCTACGAGCTTTGTGAAGCCGTGGGACCTGAGCCTACTAG
upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 3
-tatttagtttgcctgcatttatatgtctgtagaatgttatatgcaccataccaaatattcttttttatttatttatgtgatttaatttcatcctg--gatagGATAAGTCTTGGCGCGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
|| | | | | |||| || ||| || || | | | | || ||||| ||||| ||| | ||| |||| || || | |||| | |||||||| || || |||||||||||| ||||||| |||||||||||| | |||||||| |||||| |||||||
ttaaacaaatcaatatcgatgatattcaggtcattcattacatcttccgt-ctactttttactttttttttatatatat--ttttattttattgtgtgaacagGACAGATCTTGGCGTGTTCGCTACATGGTTGCAGATCAATTATATGAGCTTTGTCATGCTGTAGGGCCTGAAGCTACCAGMapped 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|254331030|gb|GR842295.1|GR842295EST: CAAGATTGTGTTGCACATATACTCCCGGTTATTGTTAACTTCTCCCAG GATAAGTCTTGGCGCGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTT
genomic: CAAGATTGTGTTGCACATATACTCCCGGTTATTGTTAACTTCTCCCAGgtacatgata ... tcctggatagGATAAGTCTTGGCGCGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTT
EST:
gi|26057519|gb|CA800433.1|CA800433EST: CACAAGATTGTGTTGCACATATACTCCCGGTTATTGTTAACTTCTCCCAG GATAAGTCTTGGCGCGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTT
genomic: CACAAGATTGTGTTGCACATATACTCCCGGTTATTGTTAACTTCTCCCAGgtacatgata ... tcctggatagGATAAGTCTTGGCGCGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccataccaaatattcttttttatttatttatgtgatttaatttcatcctggatagGATAAGTCTTGGCGCGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
atttaat putative branch site (score: 4)
tttcatcct CT-rich tract
aaatattcttttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatttagtttgcctgcatttatatgtctgtagaatgttatatgcaccataccaaatattcttttttatttatttatgtgatttaatttcatcctggatagGATAAGTCTTGGCGCGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - gtttgcc
- - - - - - -tgcattt
- - - - - - - - - - - atgtctg
- - - - - - - - - - - - - - - - - - -tatatgc
- - - - - - - - - - - - - - - - - - - - - - -ccatacc