Sequence
atgc intronic sequence ATGC exonic sequence...ttgcataagcattcgaaaaatgtattgatgctgtgttgtattatttgttagattcatgaattttccactaatcctgttgttgtttgtgaaaacaaaatagAGCAATGTCATCCCACATCGTTGGGTATCCTCGTATTGGACCGAAGAGAGAGCTTAAGTTTGCATTGGAGTCCTTCTGGGATGGGAAAACCAATGTTGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G20980.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G20980.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G30350.1 (Glycine max), 3'ss of exon 1
-----ttgcataa--gcattcgaaaaatgtattgatgctgtgttgtattatttgttagattcatgaattttccactaatcctgttgttgtttgtgaaaacaaaatagAGCAATGTCATCCCACATCGTTGGGTATCCTCGTATTGGACCGAAGAGAGAGCTTAAGTTTGCATTGGAGTCCTTCTGGGATGGGAAAACCAATGTTGAT
| |||| | || | || | |||| | | | | ||| ||| | | |||| | | || ||| || ||| | | || | ||||||||| |||| || || ||||| ||||| || || ||||| |||||||| ||||||||||| ||||| || || |||||||| || | | || ||||
tatattgatataattggatctgtaagaaatattttttatttttgaacttacttggtcg---tatgaggtattca--aattgtggatttgcattttgcaatga--cagAGCAATGGCATCTCATATTGTTGGTTATCCACGCATGGGACCCAAGAGAGAACTTAAGTTTGCTTTGGAATCTTTTTGGGATGGAAAGAGTAGTGCTGAT
upper sequence: AT5G20980.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G15140.1 (Glycine max), 3'ss of exon 1
-------ttgcataagcattcgaaaaatgtattgatgctgtgttgtattatttgttagattcatgaattttccactaatcctgttgttgtttgtgaaaacaaaatagAGCAATGTCATCCCACATCGTTGGGTATCCTCGTATTGGACCGAAGAGAGAGCTTAAGTTTGCATTGGAGTCCTTCTGGGATGGGAAAACCAATGTTGAT
| | | | | || | ||| | || | | | ||| | | | | |||| | | || ||| || ||| | | || | ||||||||| |||| || || ||||| ||||| || || ||||| |||||||| ||||||||||| ||||| || || |||||||| || | | || |||
ggaatggatataattggacctgtaagaagtacttttgatttttgaacttactcgatcg---tatgaggtattca--aattgtggacttgcgttttgcaatga--cagAGCAATGGCATCTCATATTGTTGGTTATCCACGCATGGGACCCAAGAGAGAACTTAAGTTTGCTTTGGAATCTTTTTGGGATGGAAAGAGTAGTGCTGAG
upper sequence: AT5G20980.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0009g01080.t01 (Vitis vinifera), 3'ss of exon 1
---ttgcataagcattcgaaaaatgtattgatgctgtgttgtattatttgttagattcatgaattttccactaatcctgttgttgtttgtgaaaacaaaatagAGCAATGTCATCCCACATCGTTGGGTATCCTCGTATTGGACCGAAGAGAGAGCTTAAGTTTGCATTGGAGTCCTTCTGGGATGGGAAAACCAATGTTGAT
| |||| ||| | ||| ||| | | | | | || ||| | || | | || ||| || || | | ||||||||| |||| ||||| || || ||||||||||| ||||| ||||||||||| |||||||| |||| || |||||||||||||||| | || |||
tatatatataatgatttgtggaattgcttgtccaaatagtatgattgaaatgcaatggatgg-tgttttattgatatatttg--gtgggttatggtgaggcagAGCAATGGCATCTCACATTGTGGGTTATCCTCGTATGGGACCCAAGAGAGAGCTCAAGTTTGCCCTGGAATCTTTCTGGGATGGGAAAAGTAGTGCTGAGMapped 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|19876949|gb|AU237780.1|AU237780EST: TCCCTCCCTTGCGCAACCGCCTCTCGCCGCCCCCGATTCTACGTCGCCAG AGCAATGTCATCCCACATCGTTGGGTATCCTCGTATTGGACCGAAGAGAGA
genomic: TCCCTCCCTTGCGCAACCGCCTCTCGCCGCCCCCGATTCTACGTCGCCAGgttttcttct ... aacaaaatagAGCAATGTCATCCCACATCGTTGGGTATCCTCGTATTGGACCGAAGAGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttagattcatgaattttccactaatcctgttgttgtttgtgaaaacaaaatagAGCAATGTCATCCCACATCGTTGGGTATCCTCGTATTGGACCGAAGAGAGAGCTTAAGTTTGCATTGGAGTCCTTCTGGGATGGGAAAACCAATGTTGAT
cactaat putative branch site (score: 2)
aaaacaaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgcataagcattcgaaaaatgtattgatgctgtgttgtattatttgttagattcatgaattttccactaatcctgttgttgtttgtgaaaacaaaatagAGCAATGTCATCCCACATCGTTGGGTATCCTCGTATTGGACCGAAGAGAGAGCTTAAGTTTGCATTGGAGTCCTTCTGGGATGGGAAAACCAATGTTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- -cataagc
- - - - - - - gaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt