Sequence
atgc intronic sequence ATGC exonic sequence...gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtctgtctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
Basic information
species | Glycine max |
transcript | GLYMA07G38050.2 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 21
-----------------------------gtttgatgtgtgttgatttgccaaatgaagcttga------atttagttttccattaag---atatcaag----ggtctg-----tctgatttgtgtactttgatttatggtttg--cagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
| || || | | | || | || || ||| | | || ||| || | || || | ||| | | || | | | ||| | || ||||||||||||||||||| || || |||||||| || ||||| || ||||| ||||| ||||| || |||| ||| || ||||||||||| |||||||| ||
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgatcattattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA
upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 21
---------------------------------------------------------------gtttgatgtgt-gttgatttg---ccaaatgaagcttgaatttagttttccattaag--------atatcaagggtctgtctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
| | | ||| || | ||| |||| | | | | || | | | || | || | ||||| | | || || | | |||||||||| || ||||||| |||||||| | ||| || ||||| |||| |||||| |||||||| ||||||||||||||||| ||| | |||||||| ||
gtatattttgtaaccttttctcttactgtttgtattccctactgatgacctatttaatgtgtagctgactttgttattaacttgtaaccaagtaatggattgcttacatgctgagctgagtaatggtcagatacaaaatctgttttgactaaatatgatgtcctcatcctatcagATTATGACCGAGTTATTAAGAACATTGAGAAAGGAGAAGCAAGGATATACCGGAAGGATGAGATTATGAAAGCTATTGGGAAAAAGCTAGACCGCTATAA
upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 21
gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccat-taagatatcaagggt------ctgtctgatttgtgtactttgatttatggtttgc-agATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
|| | || ||| ||| | | || | | | |||| ||| | ||||| | ||| | ||||| ||| |||||| || | | |||||||||||||||||| ||||| |||||||| ||||| |||||||||||||| || |||||||| ||||| ||||||||||||||||| |||||||||||
--ttataacattttaatt----aaaagcaact-gtttgcaattttgcatactgaagatcaaacttttcatactgacagattt-tgtgttttgatcattgttcaactagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGAATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGTTAGACCGCTACAA
upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 13
-gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtctgtctgatt-tgtgtactttgatttatg-gtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
| || | | || || ||| || | || | || || | || | ||| |||| ||| | |||||| || ||||||||||||||||||| ||||| |||||||| ||||| ||||| |||||||| || |||||||| ||||| ||||||||||||||| | |||||||||||
accattatattttttttttaataaaagcaactgtttgcata-ctgaagatcaaactttccata--ctgatggattgtgtatgttttgatcattgtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 21
gtttgatgtgtgttgatttgccaaatgaagct--tgaat-ttagttttccattaagat---------atcaagggtctg-tctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
|| | || ||| || | ||| | ||| | || | | | || | ||| || | |||| | ||| | | || ||| |||||| || ||||| || || || ||||| |||||||| |||||||| || |||||||||| ||||||||||||||||||||||| |||| |||||||
-gttagta-actttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagctctgcctcttgttttcctttgtaaaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAG
upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 21
------------------gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtctgtctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
| | | || | || | ||| || | | | || | | | | ||| | |||| | | || ||| ||||||||||| ||||| |||||||| || || |||||||| || || ||||||| || |||||||| || || |||||||| |||| |||||||
gtaagtaacacctttcaatgctaagttatgcagtgtttttacatgtttctaagtaattcctacctccaaaaagagcttatgctaagtaagtttatcatctttccctctaaatatgtagACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTAGGAAAGACGAAATCATGAAGGCCATAGGGAAGAAACTGGATCGCTACAG
upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 21
gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtct-gtctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
| ||||| | | | | ||| | | | | |||| ||||| ||| || || | | | ||||| ||| || || | | | ||||||||||||| || || || |||||||||||||| ||||| ||||| || |||||||||||||||||||||| ||||||||||||||||| ||||||||
ggttgatatattgtcagatgcatcttacaacatccattt-gtttttcatcaaaatggtgattttttcgtctgcttttaaccattaaatacaatttctccagATTATGATAGGATCATCAAGAACATTGAAAGAGGAGAGGCTAGAATTTCTAGGAAAGATGAGATCATGAAAGCAATTGGGAAGAAGTTGGATCGCTACAA
upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 21
gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtctgtctgatttgtgtactttgat-ttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
| || ||| | || ||||| | || || | |||| | | | ||| ||| || || |||||| | | ||||||| | |||||||| | || | | |||||||| ||||||| | |||||||||||||| ||||||| |||||
------------------------------------gtaagcttttccttg-----tcaagaaacatattgtttaagctgttttgctgctgtaattt--agACTACGACAGAATTTTGCGAGCCATTGAACGCGGGGAGGCTCGCATCGCAAGAAAAGATGAAATCATGAGAACTATTGGGAAGAAGCTGGACCGATACAA
upper sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 21
gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtctgtctgatttgtgtactttgat-ttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
| || ||| | || ||||| | || || | | || | | | ||| ||| || || |||||| | | ||||||| | |||||||| | || | | |||||||| ||||||| | |||||||||||||| ||||||| |||||
------------------------------------gtaagcttttccttg-----tcaagaaacatattgtttaagctgttctgctactgtaattt--agACTACGACAGAATTTTGCGAGCCATTGAACGCGGGGAGGCTCGCATCGCAAGAAAAGATGAAATCATGAGAACTATTGGGAAGAAGCTGGACCGATACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccattaagatatcaagggtctgtctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
tttgatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtctgtctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT