Sequence
atgc intronic sequence ATGC exonic sequencegtaaagcagtgagaaccgcatgttgcttgatactcattttttacatgtgttaatgctctgctaatacatattgtatttttagAAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATTCCCCCAACGCATGAAGACAGATATTTGCTCTTTATTGATGAACTACATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G58870.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 10
----gtaaagcagtgagaaccg-catgttgcttgatactcattttttacatgtgttaatgctctgctaatacatattgtatttttagAAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATTCCCCCAACGCATGAAGACAGATATTTGCTCTTTATTGATGAACTACATG
| | || | | || | || | || || | || | | | | | | | || | ||||||| || ||||| ||||| ||||| || ||||||||||||||||||| || || || ||||| ||||||||||||||| |||||||||| | ||
gtttgaacgcaagcaactatcgatagaacagtttaagaaaatgttcgtcttgggcttacattttagtgttgttcttttttccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACCCCTCCCACAACAGAAGATAGATATTTGCTCTTTGTTGATGAACTGCGTG
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G163193_T03 (Zea mays), 3'ss of exon 9
-gtaaagcagtgagaaccgcatgttgcttgatactcattttttacatgtgttaatgctctgctaatacatattgtatttt-tagAAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATTCCCCCAACGCATGAAGACAGATATTTGCTCTTTATTGATGAACTACATG
| | | || | | | | | || | |||| | || | | || || |||| ||||||| || ||||| ||||| |||||||| ||||| ||||||||||||| || || || || || |||||||| |||||| |||||||||||| ||
gtttgaacttaagcaattactgatag---aacaatctgagagaagatgtaatttgacttactttttcaatgctgaatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 11
----------gtaaagcagtgagaaccgcatg--ttgcttgatactcatt--------ttttacatgtgttaatgctctgctaatacatattgtatttttagAAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATTCCCCCAACGCATGAAGACAGATATTTGCTCTTTATTGATGAACTACATG
| ||| || || || | ||| || | | ||| | || | || |||| | ||| | ||| | | ||||| |||||||||| || || ||||||||||| ||||| ||||| |||| ||| ||||| |||| |||||||| ||||| || |||||||| | | ||
attgtgttatgaaaatcattgttaagtttcttatttgtttattgtttattaagaagatctataaggatattcatgccttactatctcgggatgt--tatcagAAACTAAGCATATTGCCTAGGTCAGGAGGGGCTTTGGGATTTACTTACACTCCTCCAACAAATGAGGACAGATACTTGCTTTTCATTGATGAGTTGCGTG
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 11
--------------------gtaaagcagtgagaaccgcatgttgcttgatactcat-tttttacatgtgttaatgctctgctaatacatattgtatttttagAAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATTCCCCCAACGCATGAAGACAGATATTTGCTCTTTATTGATGAACTACATG
| ||| || | || | || ||| || || | | | || | || |||| | || | | | | || | ||||| |||||||||| || || ||||||||||| ||||| ||||| |||| ||| ||||| |||| |||||||| ||||| || |||||||| | | ||
ttggagcctacttgtgtattgaaaatcattaagtttcttat-ttgtttattaagaaaatctataaggatattcatgccttact--ctcttggtatgttatcagAAACTAAGCATATTGCCTAGGTCAGGAGGGGCTTTGGGATTTACTTACACTCCTCCAACAAATGAGGACAGATACTTGCTTTTCATTGATGAGTTGCGTG
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 10
--------gtaaagcagtgagaaccgc-atgttgcttgatactcattttt---tacat--gtgttaatgctctgctaatacatattgtattt----ttagAAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATTCCCCCAACGCATGAAGACAGATATTTGCTCTTTATTGATGAACTACATG
|| || || | | ||||||| || | | || ||| | | | || | ||| | || |||| ||| | ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| ||||| ||| || ||||| ||||| ||| | ||||| | ||||
gtatataagttgtatcttggaaatctctatgttgcacattattagtccttaaatactttaaggatgattcagtgccttaatatcttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA18G07280.1 (Glycine max), 3'ss of exon 10
--------gtaaagcagtgagaaccgc-atgttgcttgatactcattttttacatgtgttaatgctctgctaatac------atattgtattt----ttagAAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATTCCCCCAACGCATGAAGACAGATATTTGCTCTTTATTGATGAACTACATG
|| || || | | ||||||| | | | | ||| || |||| | | ||| | || |||| ||| | ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| ||||| ||| || ||||| ||||| ||| | ||||| | ||||
gtatataagttgtatcttggaaatctctatgttgcacatcatt-agtccttaaatactttaaggatgattcaatgccttaatatgttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG
upper sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 10
---------gtaaagcagtgagaaccgcatgttgcttgatactc---attttttacatg-tgtta-atgctc---tgctaa-tacatattgtatttttagAAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATTCCCCCAACGCATGAAGACAGATATTTGCTCTTTATTGATGAACTACATG
|| | | | | | | | | ||| | | || | | | ||| ||| || ||||| | || |||| || |||| || |||||||| ||||||||||||||||||||||| |||||||| | ||| || || |||| |||||||||||||| || |||||||| ||| ||
tactaggatgtgagtccatcacatgcatacatgctttgtcattttaaatcgtccgcgtaacattagatggtccaatgctatctgtattttgtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTGMapped 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|124824268|gb|EH909134.1|EH909134EST: GCAAGTCTTCTTTCTGGACAGTCCCGTGTTGAG AAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATT
genomic: GCAAGTCTTCTTTCTGGACAGTCCCGTGTTGAGgtaaagcagt ... gtatttttagAAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatactcattttttacatgtgttaatgctctgctaatacatattgtatttttagAAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATTCCCCCAACGCATGAAGACAGATATTTGCTCTTTATTGATGAACTACATG
tgctaat putative branch site (score: 2)
tattttt putative PPT
taatacatattgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagcagtgagaaccgcatgttgcttgatactcattttttacatgtgttaatgctctgctaatacatattgtatttttagAAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATTCCCCCAACGCATGAAGACAGATATTTGCTCTTTATTGATGAACTACATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA