Sequence
atgc intronic sequence ATGC exonic sequencegtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaattttctattttcccccatttaatccattttggtcgttcttttctcactataattatgtagtgtttgattactaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
Basic information
species | Glycine max |
transcript | GLYMA03G04500.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 6
gtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaattttctattttcccccatttaatccattttggtcgttcttttctcactataattatgtagtgtttgattactaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
||| |||| | | || | |||| ||| | | | | | | || | || |||| | | | ||| || || ||| | ||| | |||||||||| |||||||||||||| |||||||||||||| || || || || |||||||||| ||||||||||| ||||||||||||||||||
-------------------------------------------------------gtaactattt-caagcttgcttgattt---tcatctgtgcatgtgcctaccaaataca-ttctgtaattgtacctaactgtttaactcattg--cactatacc--agGATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT
upper sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 5
gtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaattttctattttcccccatttaatccattttggtcgttcttttctcactataattatgtagtgtttgattactaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
|||||| | | | |||||| | | || || ||||| || ||| |||| | || ||| | || | | ||| | |||| ||||| |||||||||||||| || ||||||||||| || || || || |||||||||| ||||||||||| ||||||||||||||||||
----------------------------------------------gtaactatttcaggcttgattaattttcatctgtgcaaa------tgcctaccattttcattctgtaagattgtacc--taaatgtttaactcattt-----gcactatacc--agGACTTCAAGATTCAGAACATTGTTGGTTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT
upper sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
gtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaattttctattttcccccatttaat-ccattttggtcgttcttttctcactataattatgtagtgtttgatta---ctaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
|||| ||| | | | | ||| | ||| | || ||| ||| | ||| | |||| | ||| | |||||||||| || ||||||||||| || || ||||||||||| || || || || |||||||| ||||| ||||| ||||| || ||||| |||
--------------------------------------------------------------------------------gtaatgccactctagctcacatcaattcattcagattg-attgtccttgcttatatcagcttgacgcattgg--aacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
upper sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
gtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaattttctattttcccccatttaatccattttggtcgttcttttctcactataattatgtagtgtttgattactaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
| ||| | | || | | ||| | | | || || ||| || | || |||| | | | || || || ||||||| || |||||||| ||||| |||||||||||||||||||| || || |||| ||||| ||||||||||| |||||||| |||||||||
-----------------------------------------------------------------gtaactttttcatacttg-tgtacattgacc-tgttctttgaacaatatgtacat------cagttgctaagttgctgttc------taagcc--agGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
upper sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
gtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaattttctattttcccccatttaatccattttggtcgttcttttctcactataattatgtagtgtttgattactaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
| | ||||| | | | | | | | | || | |||| | | | | ||| | || | |||| || || |||||||| ||||| |||||||||||||| ||||| || || |||| ||||| ||||| ||||| |||||||| |||||||||
---------------------------------------------------------------------------------gtagctattttcatactcgtgtacagatctgagctttgaacaatttgtacatcagtcactaagttgc-tgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
upper sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
gtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaattttcta---ttttcccccatttaatccattttggtcgttcttttctcactataattatgtagtgtttgattactaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
|| || || | || ||| ||| || || |||||| |||||| ||| | || || |||||| | | || || || |||||||||| |||||||| ||||| || |||||||||||||| ||||| ||| | || || |||||||| || || || | |||||||||||||
-------------------------------------------------------gtacaatttctttaaaccttttccctatccaa--catttt--------ttttcttacttt----------tgctta--tactaaatatattcaattgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
upper sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
gtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaattttctattttcccccatttaatccattttggtcgttcttttctcactataattatgta-gtgtttgat-tactaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
| |||||| | || | | ||| | | | ||| |||| | || | || || || | || |||| || | | | || || | | || |||| | || || || | ||||||| || || ||||||||||| ||||| ||||||||||| |||||||| |||| || ||||||||||| || ||| ||||||||||||||
---------------gtactcatatgtctctctctggtcctgatccagcacacact--gtgttattcatttttatctcaatcaa--caattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattac-attttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
upper sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
gtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaatttt-ctattttcccccatttaatccattttggtcgttcttttctcactataattatgtagtgtttgattactaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
| | | ||| | | || | | || | | | |||| || || | || | | ||| |||| |||| | |||| | | || || | || || | | |||| ||| |||||||| || ||||||||||| || ||||| |||||||| || ||||||||| |||| || || ||||||||||| |||||||| || || ||
----------------------------gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattc-ttctccttgtttttttgccactgttcttattttatatt-gactgctgttttttattgtggg----atg---tagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
upper sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 5
-----gtactgcttctgctc----tttctcataat----ctttgctgaaattattgaa---aagcgctattttaaaaattttctattttcccccatttaatc-cattttggtcgtt--cttttctcactataatta--tgtagtgtttgattactaattggttctttg----ggtattatgcttt--agGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
| ||||| || ||||||| ||| | || | | || | || | | ||| || | ||||| | || | |||||||||| | ||| ||| | || | ||| | | | || | | ||| | | || |||| |||| |||||||||||||| ||||| || || ||||| || |||||||| || ||||| |||||| | |||||| |||||||| ||| ||||||
gtaatttcgtgcttaggcatagagtttctcagaataatgcatttcatgttgtgttagatgcaaactcgttttcaagtaccgattatttgaagtattgtagttgcattttggtcactgccttctctggattcaacaagatgtgatttgcggtttcagagatgttgctgacaaagttacctctctttgcagGACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGTMapped 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|31461676|gb|CD403704.1|CD403704EST: TATGCTCGTATTATCCNAAAACTTGGCTTCCCTGCCNAATTTAAG GATTTCNAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATA
genomic: TATGCTCGTATTATCCAAAAACTTGGCTTCCCTGCCAAATTTAAGgtactgcttc ... tatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATA
EST:
gi|27445915|gb|CA953038.1|CA953038EST: TATGCCCGTATTATCCAAAAGCTTGGCTTCCCTGCCAAATTTAAG GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATA
genomic: TATGCTCGTATTATCCAAAAACTTGGCTTCCCTGCCAAATTTAAGgtactgcttc ... tatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATA
EST:
gi|254322493|gb|GR837907.1|GR837907EST: TATGCTCGTATTATCCAAAAACTTGGCTTCCCTGCCAAATTTAAG GATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATA
genomic: TATGCTCGTATTATCCAAAAACTTGGCTTCCCTGCCAAATTTAAGgtactgcttc ... tatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actataattatgtagtgtttgattactaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
tactaat putative branch site (score: 1)
tttgattactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaattttctattttcccccatttaatccattttggtcgttcttttctcactataattatgtagtgtttgattactaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG