Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcatatgcttattggcaatcaaatcagtttctgatgtcttcaagatataaaattcctatgtaagaacgaatctgtaacttcattgactgtcctactatttttttctagGCAAAGAACATGCTCTTGTCGTTTGTAATCACCGAAGTGATATTGATTGGCTTGTGGGATGGATTCTGGCTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G57650.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 1
gtaagttcatatgcttattggcaatcaaatcagtttctgatgtcttcaagatataaaattcctatgtaagaacgaatctgtaacttcattgactgtcctactatttttttctagGCAAAGAACATGCTCTTGTCGTTTGTAATCACCGAAGTGATATTGATTGGCTTGTGGGATGGATTCTGGCTCAG
||||| | ||| | | || || | ||||| | || | || | || || || | | | || | | || | || ||| ||| ||||| ||||| || ||| | | ||||| ||||||||||||||||||||| | |||||||| |||| |||
gtaagg--agccctccattaatatttccattgtttgcattcaccttca---tgcaag---cttaaggaaaaaaagattgg--attacaa-gcttatctgaataatttcac--agGTAAAGAGCATGCACTCGTCATATCAAATCATCGAAGTGATATTGATTGGCTTATTGGATGGATATTGGCCCAG
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G32420.1 (Glycine max), 3'ss of exon 3
----------------------------------------------gtaagttcatatgcttattggcaatcaaatc--agtttctgatgtcttcaagatataaaattcctatgtaagaacgaatctgtaacttcattgact--gtcctactatttttttctagGCAAAGAACATGCTCTTGTCGTTTGTAATCACCGAAGTGATATTGATTGGCTTGTGGGATGGATTCTGGCTCAG
| ||| | | | ||| || | || | |||| ||| | ||| | | | ||| | || | | | | | || || | | | || ||| ||||| ||||| ||||| | | |||||| |||||||||||||||||||||| |||||| || ||||||
gtaagtcttttgttagcctatgatttagcactaagcactttactccctccattctttcgtgtgttgtacatgtattcttatcttctagaaaggaaaaggggggaggttcttggg--acaacatttgcttacatataataatttggttctgttttgtattatcagGTAAAGAGCATGCACTTGTGATAAGCAATCACAGAAGTGATATTGATTGGCTTGTTGGATGGGTTTCAGCTCAG
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G29600.1 (Glycine max), 3'ss of exon 3
--------------------------------------gtaagttcatatgcttattggcaatcaaatcagttt---ctgatgtcttcaagatataaaattcctatg----taagaacga-atctgtaacttcat--tgact--gtcctactatttttttctagGCAAAGAACATGCTCTTGTCGTTTGTAATCACCGAAGTGATATTGATTGGCTTGTGGGATGGATTCTGGCTCAG
| | | | | | || | || | || | | | ||||| ||| | ||| | | | || | || || | || | | | | || | | | || ||| ||||| ||||| ||||| | | |||||| |||||||||||||||||||||| |||||| || ||||||
gtaagccttttgttagcctatgatttagcactaagcaatttactccctccattctttctccatgtgttgtgtatgcattcttatcttctagaaaggaaaagggggaggttcttgggacaacatttgcttccatataataatttgattctgttttgtattatcagGTAAAGAGCATGCACTTGTGATAAGCAATCACAGAAGTGATATTGATTGGCTTGTTGGATGGGTTTCAGCTCAG
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G31320.1 (Glycine max), 3'ss of exon 3
gtaagttcatatgcttattggcaatcaa-atcagtttctgatgtcttcaagatataaaattcctatgtaagaacgaatctgtaacttcattgactgtcctactatttttttctagGCAAAGAACATGCTCTTGTCGTTTGTAATCACCGAAGTGATATTGATTGGCTTGTGGGATGGATTCTGGCTCAG
|||||| | ||| ||| | | || || || | || ||| | || || | | ||| ||||| || ||||| ||| ||||| |||||||||||| | | |||||| ||||||| |||||||||||||| |||||| || | ||||||
gtaagtctcttgtactat--gcatttagtgctaggctcacccccctccc---cccaattttcgttcgt---------cttgaattctgatt--ctgtc----tagaattttccagGTAAAGAGCATGCTCTTGTCATATCCAATCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTAGCTCAG
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 3
gtaagttcatatgctt--attggcaatcaaatcagtttctgatgtcttcaagatataaaatt-cctatgtaagaacgaatctgtaacttcattgactg-tcctactatttttttctagGCAAAGAACATGCTCTTGTCGTTTGTAATCACCGAAGTGATATTGATTGGCTTGTGGGATGGATTCTGGCTCAG
||||| ||| | ||| || ||| | |||| | | || | | | || ||| || | |||| | || |||| || | | | |||||| ||| ||||||||||| ||| | | | || ||| ||||||| |||||||||||||| |||||| || ||||||||
gtaaggtcaaaaacttttatgggctgagtgctgggttttccctcaaaggaggaaagatattttcctgtgcagtgctgaat--acatttttattggctaatgttggtgagtttttc-agGTAAAGAACATGCACTTCTTATATCAAACCACAGAAGTGACATTGATTGGCTTGTTGGATGGGTTTTGGCTCAG
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S72_209V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaagttcat--atgcttattggcaatcaaat--cagttt---ctgatgtcttcaagatataaaattcctatgtaagaacga-atctgtaacttcattgactgtcctactatttttttctagGCAAAGAACATGCTCTTGTCGTTTGTAATCACCGAAGTGATATTGATTGGCTTGTGGGATGGATTCTGGCTCAG
|| |||| | || || | || | | | ||| || |||| | | | | || | || | | | || ||||| || | | || | || | || || ||| || || || || | || ||||||||||||| ||||| ||||||||||| || ||||||||| | || |||
gtcagttggtgaattgttgtgaagtattgatttgcgattttgactaatgtttcagtgttttggaactgctcgggatgcctgatatctgaaaagtgg--gcttggtttcctgtgttcgtc-agGAAAGGAGCACGCATTACTCATTTGTAATCACCGCAGTGACATTGATTGGCTCGTAGGATGGATTATTGCCCAGMapped 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|116460345|gb|EG502937.1|EG502937EST: ATCCAAGTGTTTGCTGATAATGAGGCCTTCAATCGAATGG GCAAAGAACATGCTCTTGTCTTTTGTAATCACCGA
genomic: ATCCAAGTGTTTGCTGATAATGAGACCTTCAATCGAATGGgtaagttcat ... ttttttctagGCAAAGAACATGCTCTTGTCGTTTGTAATCACCGA
EST:
gi|124860313|gb|EH944750.1|EH944750EST: CTGATAATGAGACCTTCAATCGAATGG GCAAAGAACATGCTCTTGTCGTTTGTAATCACCGAAGTGTTATTGATTGGC
genomic: CTGATAATGAGACCTTCAATCGAATGGgtaagttcat ... ttttttctagGCAAAGAACATGCTCTTGTCGTTTGTAATCACCGAAGTGATATTGATTGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctatgtaagaacgaatctgtaacttcattgactgtcctactatttttttctagGCAAAGAACATGCTCTTGTCGTTTGTAATCACCGAAGTGATATTGATTGGCTTGTGGGATGGATTCTGGCTCAG
cattgac putative branch site (score: 3)
tcctactatttttttc putative PPT
tactatttttttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcatatgcttattggcaatcaaatcagtttctgatgtcttcaagatataaaattcctatgtaagaacgaatctgtaacttcattgactgtcctactatttttttctagGCAAAGAACATGCTCTTGTCGTTTGTAATCACCGAAGTGATATTGATTGGCTTGTGGGATGGATTCTGGCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA