Sequence
atgc intronic sequence ATGC exonic sequencegtttgttttcaactctcttttaagctgttttcttattattaacattttcaggaaaaaaaaggaattctataatttaatccttaggattgcttcagGTTATATTAACACCAACCCATTTAGCCATTGTTATGGAATATGCATCTGGAGGAGAACTTTTCGAGCGAATCTGCAATGCAGGCCGCTTCAGCGAAGACG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G33950.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 2
----gtttg--ttttcaactctcttttaagctgttttcttattattaacattttcaggaaaaaaaaggaattctataatttaatccttaggattgcttcagGTTATATTAACACCAACCCATTTAGCCATTGTTATGGAATATGCATCTGGAGGAGAACTTTTCGAGCGAATCTGCAATGCAGGCCGCTTCAGCGAAGACG
|| | | |||| | || | || || ||| || |||||| | ||||| | | ||||| || || || |||||||| ||||| ||||| ||| | || ||||| ||||||||||| ||||| || || ||||||||| |||| || || | || ||||| ||||| |
gtaagtcaggatcttcatgacgctcattctctagttcaccatt--caatattttccagcaaaaataagttctctatcatgtat------------ctacagGTTATTTTAACCCCAACTCATCTTGCTATTGTCATGGAATATGCCTCTGGTGGTGAGCTTTTCGAGAGAATTTGTAAGAATGTACGGTTCAGTGAAGATG
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G171435_T01 (Zea mays), 3'ss of exon 2
gtttgttttcaactctcttttaagctgttttcttattattaacattttcaggaaaaaaaaggaattctataatttaatccttaggattgcttcagGTTATATTAACACCAACCCATTTAGCCATTGTTATGGAATATGCATCTGGAGGAGAACTTTTCGAGCGAATCTGCAATGCAGGCCGCTTCAGCGAAGACG
| | || | || | | | | ||| | ||| | || | ||||| ||| | || || ||||||| |||||||| |||||| | || ||||| ||||||||||| ||||| || || ||||| ||| |||| || || | || ||||| ||||| |
--------gtgagttgggattgtgatgctgtttctcccccagaattcatttgttaaacac----ttttgaaattt----ctttgtatatct--agGTTATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATG
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G33120.1 (Glycine max), 3'ss of exon 2
gtttgttttcaactctcttttaagctgttttcttattattaacattttcaggaaaaaaaaggaattctataatttaatccttaggattgcttcagGTTATATTAACACCAACCCATTTAGCCATTGTTATGGAATATGCATCTGGAGGAGAACTTTTCGAGCGAATCTGCAATGCAGGCCGCTTCAGCGAAGACG
|| | ||| | || || | | || |||| | | | | | || | || ||| | | | | | ||| |||||||||| || ||||| |||||||| ||||| ||||||||||| ||||||||||| || || ||| |||| ||||||||||| | ||||| || || |
----gtgtgcaaacccct---aatgtctgatcctatttctttctatcttaaaaata--------ttttattaatcgttttctgatgtgactttagGTTATATTGACCCCAACACATTTAGCAATTGTGATGGAATATGCTTCTGGAGGAGAGCTATTTGAGAGAATATGCAATGCAGGAAGGTTCAGTGAGGATG
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 2
gtttgttttcaactctcttttaagctgttttcttattattaacattttcaggaaaaaaaaggaattctataatttaatccttaggattgcttcagGTTATATTAACACCAACCCATTTAGCCATTGTTATGGAATATGCATCTGGAGGAGAACTTTTCGAGCGAATCTGCAATGCAGGCCGCTTCAGCGAAGACG
|| | || ||||||| | || || |||| | | | | || || | || | || | | || | ||| |||||||||| |||||||| ||||| || ||||| ||||||||||| ||||||||||| || || ||| |||| ||||||||||| | ||||| || || |
----gtgtgtaaa---cttttaatgtcttatcctatttcttcctatcttagaaata--------ttgtttagtccttttctgttg-cgactttagGTTATATTGACACCAACACATTTGGCAATTGTGATGGAATATGCTTCTGGAGGAGAGCTATTTGAGAGAATATGCAATGCAGGGAGGTTCAGTGAGGATG
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 2
gtttgttttcaactctcttttaagctgttttcttattattaacattttcaggaaaaaaaagga------attctataatttaat---ccttaggattgcttcagGTTATATTAACACCAACCCATTTAGCCATTGTTATGGAATATGCATCTGGAGGAGAACTTTTCGAGCGAATCTGCAATGCAGGCCGCTTCAGCGAAGACG
||| | || || || || | |||||||| | || || ||| ||||||| || ||| | || |||||||||| ||||||||||| | || ||||| ||||||||||| ||||||||||| || || ||||| || |||||||| ||||| ||||| || || |
------------gtctggtcgaaa-tgaatttttcccaaccacattttctatccagtgaatgattctcagttcaataattttatgttttttaatcatactctagGTTATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATG
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S240_91V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------gtttgttttcaactctcttttaagctgttttcttattattaacattttcaggaaaaaaaaggaattctataatttaatccttaggattgcttcagGTTATATTAACACCAACCCATTTAGCCATTGTTATGGAATATGCATCTGGAGGAGAACTTTTCGAGCGAATCTGCAATGCAGGCCGCTTCAGCGAAGACG
|||| | | | | | | || || || || | ||||| | || | ||| | ||| | || | | | | | | ||||||| | || |||||||| ||||||||||| || ||||| ||||| |||| |||||||| ||||||||||| || |||||||| || ||||| ||||| |
gtgatttttctaggcggttgtttttgctttcacgggtttgagaactttggatatatgaatgtatcga-ttggattggtaatactggaattttttg-aacattttggagtactaaatcttgtacttca--actacctcagGTTCTGTTGACACCAACTCATTTAGCCATCGTGATGGAGTATGCTGCTGGTGGAGAACTGTTCGAGCGAATTTGTAATGCAGGTCGGTTCAGTGAAGATG
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------gtttg---ttttcaactctc--ttttaagctgttttcttattattaacattttcaggaaaaaaaaggaattctataat-ttaatcctta-----ggattgcttcagGTTATATTAACACCAACCCATTTAGCCATTGTTATGGAATATGCATCTGGAGGAGAACTTTTCGAGCGAATCTGCAATGCAGGCCGCTTCAGCGAAGACG
|| || | || || | | | || | | ||| ||||| | | | | | ||| | | ||| ||| | | | ||||| | || || || |||||||| || |||||||| ||||||||||| |||| ||||| || || |||||||| || || |||| ||| ||||| ||||| |
gtgatcattctagactttttgattttttattattattaatttttttttccctgaacttgtagaccctgggtgtgtggatgaactttctggattgacattactggaagatattggacatttaggagtactaaagcttgtacttgaactatttcagATCATGTTGACTCCAACCCACTTGGCCATTGTGATGGAATATGCTGCTGGTGGAGAGCTGTTTGAGCGAATTTGTAAAGCAGTCCGGTTCAGTGAAGATG
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------gtttgttttcaactctcttttaagctgttttcttattattaacattttcaggaaaaaaaaggaattctataatttaatcct----taggattgcttcagGTTATATTAACACCAACCCATTTAGCCATTGTTATGGAATATGCATCTGGAGGAGAACTTTTCGAGCGAATCTGCAATGCAGGCCGCTTCAGCGAAGACG
||||| | | | | | || | |||||| | | | || || ||| || | | | | ||||||| || | || ||||||||||| || ||||||||||||||||| |||| ||||||||||| ||||||||||| || |||||||||||||| ||||| |
gtgagaaacctacacatatttcttattattccaagggtctcaagatttgtggccggtcgcacaatgatgtacctactgg--actaacatgattgtcttattgtacattttgtagcattgaaactcgtacttgtttcatttcagGTCATGCTGACTCCAACCCATTTGGCTATTGTTATGGAATATGCTGCTGGTGGAGAACTTTTTGAGCGAATCTGTAACGCAGGCCGCTTCAGTGAAGATG
upper sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S113_72V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------gtttgttttcaactctcttttaagctgttttcttattattaacattttcaggaaaaaaaaggaattctataatttaatccttaggattgcttcagGTTATATTAACACCAACCCATTTAGCCATTGTTATGGAATATGCATCTGGAGGAGAACTTTTCGAGCGAATCTGCAATGCAGGCCGCTTCAGCGAAGACG
| | |||| | || ||| | || ||| | | ||| ||| | ||| ||| | | || | || ||||||| || || || || |||||||| |||||||| ||||||||||| | || ||||| || || |||||||| || ||||| || || ||||||||||| |
gtgtgaaagaagcagctctttcgtattttgcagaggttttggaatctattttgcatggataaatattctggcatgacatggttagctccctgttacaaattctggagtgcta-aatcttgtgctc--gtttcattcagGTCATGTTGACCCCGACCCATTTGGCCATTGTGATGGAATATGCGGCGGGTGGAGAGCTGTTTGAGCGAATTTGTAATGCTGGTCGGTTCAGCGAAGATGMapped 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|125276865|gb|EL290950.1|EL290950EST: TCCTTAAGACATCCCAATATCGTTAGATTCAAAGAG GTTATATTAACACCAACCCATTTAGCCATTGTTATGGAATATGCATCTGGA
genomic: TCCTTAAGACATCCCAATATCGTTAGATTCAAAGAGgtttgttttc ... attgcttcagGTTATATTAACACCAACCCATTTAGCCATTGTTATGGAATATGCATCTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacattttcaggaaaaaaaaggaattctataatttaatccttaggattgcttcagGTTATATTAACACCAACCCATTTAGCCATTGTTATGGAATATGCATCTGGAGGAGAACTTTTCGAGCGAATCTGCAATGCAGGCCGCTTCAGCGAAGACG
ttgcttc CT-rich tract
aaaaaaaaggaattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttttcaactctcttttaagctgttttcttattattaacattttcaggaaaaaaaaggaattctataatttaatccttaggattgcttcagGTTATATTAACACCAACCCATTTAGCCATTGTTATGGAATATGCATCTGGAGGAGAACTTTTCGAGCGAATCTGCAATGCAGGCCGCTTCAGCGAAGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA