Sequence
atgc intronic sequence ATGC exonic sequencegtatttttaacatttcctttgctcagtcaaagaagtatgctactaattcctctgttgattagtttgggattgtttctgtagGTTGGTCTATTGAATGTTGATGGGTACTATAACAATTTGCTTGCTTTATTTGATACCGGTGTCGAAGAAGGTTTTATCAAGCCAGGTGCACGTAACATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G11950.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 5
gtatttttaacat--ttcctttgctcagtcaaagaagtatgctactaattcctctgttgattagtttgggattgtttctgt--agGTTGGTCTATTGAATGTTGATGGGTACTATAACAATTTGCTTGCTTTATTTGATACCGGTGTCGAAGAAGGTTTTATCAAGCCAGGTGCACGTAACATTG
|||||| | ||| ||| || | || || || | || | ||| | ||| ||||||||||| |||||||||| || ||||||||| ||||||||| |||||||| | ||||| |||||||||| || ||||| ||||||| || || |
------gtaacatagtatttttactctgtagtacaaaatctttaatataacaatcaagtgctaactcaaaattcatactgcacagGTTGGTCTACTGAATGTTGACGGTTACTATAACTGTTTGCTTGCATTATTTGACAATGGTGTTAAAGAAGGTTTCATTAAGCCTTGTGCACGGAATATAG
upper sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G05560.1 (Glycine max), 3'ss of exon 5
gtatttttaacatttcctttgctcagtcaaagaagtatgctactaattcctctgttgattagtttgggattgtttctgt--agGTTGGTCTATTGAATGTTGATGGGTACTATAACAATTTGCTTGCTTTATTTGATACCGGTGTCGAAGAAGGTTTTATCAAGCCAGGTGCACGTAACATTG
||| | | |||| || ||| || | | || ||| || || | ||| | ||| ||||||||||| |||||||||| || ||||||||| ||||||||| |||||||| | ||||| ||||||| || || ||||| ||||||| | || |
gtaacat-agtatttttactgtgtagtacaaagtctttaata-taacaatcaagt--gctaactcaatattcatactgcacagGTTGGTCTACTGAATGTTGACGGTTACTATAACTGTTTGCTTGCATTATTTGACAATGGTGTTAAAGAAGGCTTCATTAAGCCTTGTGCACGGGATATAG
upper sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G34510.1 (Glycine max), 3'ss of exon 5
gtatttttaacatttcctttgctcagtcaaagaagtatgctactaattcctctgttgattagtttgggattgtt-tctgtagGTTGGTCTATTGAATGTTGATGGGTACTATAACAATTTGCTTGCTTTATTTGATACCGGTGTCGAAGAAGGTTTTATCAAGCCAGGTGCACGTAACATTG
||| | | | | || | ||| | ||||||| | || | | || | || ||||||||||| | ||||||||||| ||||||||| |||||| || |||||||| | ||||| |||||||| || || |||| ||||| || || ||
gtaacctgatgttgttacttagtagtataaatccttgctatactaatataatcatgtgctaactcagaatcatcctccacagGTTGGTCTACTCAATGTTGATGGTTACTATAACTCTTTGCTCGCATTATTTGACAATGGTGTTGAAGAAGGCTTCATTAAGCATGGTGCTCGGAATATAC
upper sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0008g01040.t01 (Vitis vinifera), 3'ss of exon 5
-------------------gtatttttaacatttcctttgc-tcagtcaaagaagtatgctactaattcctctgttgattagtttgggattgtttc-tgtagGTTGGTCTATTGAATGTTGATGGGTACTATAACAATTTGCTTGCTTTATTTGATACCGGTGTCGAAGAAGGTTTTATCAAGCCAGGTGCACGTAACATTG
| | ||| | | || | | || || | ||| || | | ||| || || ||| | |||||||||| | ||||||||||||||||| ||| ||||||||| |||||||| | ||||||| ||||||| || |||||||||||||| || | || |
tatagatcaaaaatgcaaaatcctgttagagtggcaatttcatgagagaatattggatgaggtgaacaataatatc--ttaattaggcattactctacacagGTTGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTTGACAACGGTGTCAAAGAAGGCTTCATCAAGCCAGGTGCTCGGCATATAGMapped 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|19874754|gb|AU235585.1|AU235585EST: AGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG GTTGGTCTATTGAATGTTGATGGGTACTATAACAATTTGCTTGCTTTATTT
genomic: AGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACGgtatttttaa ... gtttctgtagGTTGGTCTATTGAATGTTGATGGGTACTATAACAATTTGCTTGCTTTATTT
EST:
gi|19740964|gb|AU226317.1|AU226317EST: AGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG GTTGGTCTATTGAATGTTGATGGGTACTATAACAATTTGCTTGCTTTATTT
genomic: AGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACGgtatttttaa ... gtttctgtagGTTGGTCTATTGAATGTTGATGGGTACTATAACAATTTGCTTGCTTTATTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaagaagtatgctactaattcctctgttgattagtttgggattgtttctgtagGTTGGTCTATTGAATGTTGATGGGTACTATAACAATTTGCTTGCTTTATTTGATACCGGTGTCGAAGAAGGTTTTATCAAGCCAGGTGCACGTAACATTG
ttgtttct CT-rich tract
tactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttttaacatttcctttgctcagtcaaagaagtatgctactaattcctctgttgattagtttgggattgtttctgtagGTTGGTCTATTGAATGTTGATGGGTACTATAACAATTTGCTTGCTTTATTTGATACCGGTGTCGAAGAAGGTTTTATCAAGCCAGGTGCACGTAACATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG