Sequence
atgc intronic sequence ATGC exonic sequencegttttatgcttttagctttttcctcacaattttagtgttcaattgcatttcgttattaactcttggtttttgtgtgtgtgtgttgactgctctatgaacagatcaggtaaattatcaatcttttgtgtatcttgtaacttttagatttgtctagaggaataaatggttttatgagattttgtggttttggtttagGGACATTGTGGTTCTTGCTGGGCATTTGGTGCTGTTGAATCACTATCAGATAGATTCTGTATCCAATTTGGCATG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01610.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G01610.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G41120.1 (Glycine max), 3'ss of exon 5
gttttatgcttttagctttttcctcacaattttagtgttcaattgcatttcgttattaactcttggtttttgtgtgtgtgtgttgactgctctatgaacagatcaggtaaattatcaatcttttgtgtatcttgtaacttt---tagatttgtctagaggaataaatggtttt--atgagattttgtggttttggtttagGGACATTGTGGTTCTTGCTGGGCATTTGGTGCTGTTGAATCACTATCAGATAGATTCTGTATCCAATTTGGCATG
|||| | ||| ||| | || | |||| || ||| | ||| ||| ||||| ||||| | || || |||| || ||||||||||| |||||||||||||||||||||||| | |||||| | || || || || |||| |
----------------------------------------------------------------------------------------------------------gtaa-tcctcatattttctcaca-ctaacatctttaaatacattcaattcaaggttcaaagagttttcagctgatccttgtgctgatgattcagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTA
upper sequence: AT4G01610.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 5
gttttatgcttttagctttttcctcacaattttagtgttcaattgcatttcgttattaactcttggtttttgtgtgtgtgtgttgactgctctatgaacagatcaggtaaattatcaatcttttgtgtatcttgtaacttttagatttgtctagaggaataaatggttttatgagatt--------ttgtggttttggtttagGGACATTGTGGTTCTTGCTGGGCATTTGGTGCTGTTGAATCACTATCAGATAGATTCTGTATCCAATTTGGCATG
|| | || || | | || | |||| || | | | | || | || || ||| ||||| | || || |||| || ||||||||||| |||||||||||||||||||||||| | |||||| | || || || || |||| |
----------------------------------------------------------------------------------------------------------gtgatcctcatattttct---cacactgacatctttaaatacattcaatgttaaaagagtttctagctgatccttcatccttgtgctgatgattcagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT
upper sequence: AT4G01610.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0005g02820.t01 (Vitis vinifera), 3'ss of exon 4
gttttatgcttttagctttttcctcacaattttagtgttcaattgcatttcgttattaactcttggtttttgtgtgtgtgtgttgact-gctctatgaacagatcaggtaaattatcaatcttttgtgtatcttgtaacttttagatttgtctagaggaataaatggttttatgagattttgtggttttggtttagGGACATTGTGGTTCTTGCTGGGCATTTGGTGCTGTTGAATCACTATCAGATAGATTCTGTATCCAATTTGGCATG
|| ||| | || | | || | ||| ||| | | || | | ||| | ||| | || ||||| |||| | |||| | |||| |||||||| ||||| ||||| ||||||||||||||||| || |||||| | || |||||||| |||||||||
-----------------------------------------------------------------------------gtaacttggtttgcattttatttagcgttgtccctatataaatgaatgaggaattctcagaaatttgggtttattta--------------tttatttatttttatt-ttttaaatcagGGTCATTGTGGCTCTTGTTGGGCTTTTGGTGCTGTTGAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATGMapped 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|86059238|gb|DR354995.1|DR354995EST: CTAGAACTGCTTGGCCACAGTGCACTAGTATTGGAAACATCTTAGATCAG GGACATTGTGGTTCTTGCTGGGCATTTGGTGCTGTTGAATCACTATCAGAT
genomic: CTAGAACTGCTTGGCCACAGTGCACTAGTATTGGAAACATCTTAGGTTTGgttttatgct ... tttggtttagGGACATTGTGGTTCTTGCTGGGCATTTGGTGCTGTTGAATCACTATCAGAT
EST:
gi|301501566|gb|HO207106.1|HO207106EST: CTAGAACTGCTTGGCCACAGTGCACTAGTATTGGAAACATCTTAGATCAG GGACATTGTGGTTCTTGCTGGGCATTTGGTGCTGTTGAATCACTATCAGAT
genomic: CTAGAACTGCTTGGCCACAGTGCACTAGTATTGGAAACATCTTAGGTTTGgttttatgct ... tttggtttagGGACATTGTGGTTCTTGCTGGGCATTTGGTGCTGTTGAATCACTATCAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagatttgtctagaggaataaatggttttatgagattttgtggttttggtttagGGACATTGTGGTTCTTGCTGGGCATTTGGTGCTGTTGAATCACTATCAGATAGATTCTGTATCCAATTTGGCATG
aataaatggttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttatgcttttagctttttcctcacaattttagtgttcaattgcatttcgttattaactcttggtttttgtgtgtgtgtgttgactgctctatgaacagatcaggtaaattatcaatcttttgtgtatcttgtaacttttagatttgtctagaggaataaatggttttatgagattttgtggttttggtttagGGACATTGTGGTTCTTGCTGGGCATTTGGTGCTGTTGAATCACTATCAGATAGATTCTGTATCCAATTTGGCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT