Sequence
atgc intronic sequence ATGC exonic sequence...gtgtatatatgtgtgtttgtatgtggaatgtgttttcaccaaactaagtccccattttgatttgattagttttcctttgacttgatttgatcccaaacagGATAAGTCGTGGCGTGTGCGGTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
Basic information
species | Glycine max |
transcript | GLYMA02G10790.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------------------------------------gtgtatatatgtgtgtttgtatgtggaatgtgttttcaccaaactaagtccc----cattttgatt--tgattagt--tttcctttgact-tgatttgatcccaaa-cagGATAAGTCGTGGCGTGTGCGGTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
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gtatatcttacacacttttggtggcttaataaatgttgggagaaaagataaagttgtcaatactaattctcgtaaaaattactagagtaagatttccataag-atctgctactagacaataatttcatgtgcttaagtttcagcacactaccatacatggttaatgatttcaattgcttatgttttcttaacatctcagGATAAATCTTGGCGTGTGCGCTATATGGTGGCAAATCAACTGTATGAACTATGTGAAGCTGTTGGTACTGAACCCACAAG
upper sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 4
gtgtatatatgtgtgtttgtatgtggaatgtgttttcaccaaact--------aagtccccattttgatttgatta----gttttcctttgacttgatttgatcccaaacagGATAAGTCGTGGCGTGTGCGGTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
|| ||| ||||||| | | || | | | | || ||| | ||| || | | ||| |||| || || | | ||||||||||| ||||||||||| || |||||||||||||| | ||||| ||||||||||||||||| || || || || ||
gtaaataaatgtgtgaatatgataaaaaaattctattgatgagctttatgggaaagctgtaaggcagatatgtatgagctgctttatcttgatttttttcgtctttgagcagGATAAGTCCTGGCGTGTGCGTTATATGGTTGCAAATCAGCTCTATGAACTTTGTGAAGCTGTAGGACCGGAGCCAACTAG
upper sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgtatatatgtgtgtttgtatgtggaatgtgttttcaccaaactaagtccccattttgatttgattagttttcctttgacttgatttgatcccaaacagGATAAGTCGTGGCGTGTGCGGTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
||| || | | || | | ||| | | || ||||| | || | || || |||| ||| | | | ||||||||||| ||||||||||| || ||||||||||||||| | || |||||||||||||| || || ||||| ||||| ||
------------gtgattatgtctgtag-gcttttatgctga---tgatctacatttaaaagaaatgcttaatctttgtactt--tttca--ctgagcagGATAAGTCTTGGCGTGTGCGCTATATGGTTGCAAATCAACTCTACGAGCTTTGTGAAGCCGTGGGACCTGAGCCTACTAG
upper sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 3
gtgtatatatgtgtgtttgt-atgtggaatgtgttttcaccaaactaagtccccattttgatttgattagttttcctttgacttgatttgatccca--aacagGATAAGTCGTGGCGTGTGCGGTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
| | | || | | | || | | || || | ||| | |||| ||| || || | | || |||| || ||||||| | || |||||||| || |||||||||||| ||||||| |||||||||||| | |||||||| |||||| |||||||
ttaaacaaatcaatatcgatgatattcaggtcattcattacatcttccgtctactttttacttttttt---ttatatatatttttattttattgtgtgaacagGACAGATCTTGGCGTGTTCGCTACATGGTTGCAGATCAATTATATGAGCTTTGTCATGCTGTAGGGCCTGAAGCTACCAGMapped 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|192325432|gb|FK017188.1|FK017188EST: CACAAGATTGCATCACACATATACTACCGGTTATTGTCAACTTCTCGCAG GACAAGTCGTGGCGTGTGCGGTACATGGTTGCAAATCAATTGTATGAGCTT
genomic: CACAAGATTGCATCACACATATACTACCGGTTATTGTCAACTTCTCGCAGgtgtattttt ... tcccaaacagGATAAGTCGTGGCGTGTGCGGTACATGGTTGCAAATCAATTGTATGAGCTT
EST:
gi|7146818|gb|AW508740.1|AW508740EST: CACAAGATTGCATCACACATATACTACCGGTTATTGTCAACTTCTCGCAG GATAAGTCGTGGCGTGTGCGGTACATGGTTGCAAATCAATTGTATGAGCTG
genomic: CACAAGATTGCATCACACATATACTACCGGTTATTGTCAACTTCTCGCAGgtgtattttt ... tcccaaacagGATAAGTCGTGGCGTGTGCGGTACATGGTTGCAAATCAATTGTATGAGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtccccattttgatttgattagttttcctttgacttgatttgatcccaaacagGATAAGTCGTGGCGTGTGCGGTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
attttgatttgatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtatatatgtgtgtttgtatgtggaatgtgttttcaccaaactaagtccccattttgatttgattagttttcctttgacttgatttgatcccaaacagGATAAGTCGTGGCGTGTGCGGTACATGGTTGCAAATCAATTGTATGAGCTTTGTGAAGCTGTAGGCCCTGAACCTACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - -tgtgtgt
- - - - - - - - -tgtatgt
- - - - - - - - - - - - -gaatgtg
- - - - - - - - - - - - - - - - - - - ccaaact
- - - - - - - - - - - - - - - - - - - - - - - - -ccccatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg