Sequence
atgc intronic sequence ATGC exonic sequenceCCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATTgtaggttgctacaactcttcaaaaatttatggataaaagaatcaaattctttatgttattcttttggttcttggggactacatattatttgatgaatgattttaatggtaaaacatttacag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G26150.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G26150.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os05g01040.1 (Oryza sativa), 5'ss of exon 3
CCGCAGGA-ACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATTgtag-gttgctacaactcttcaaaaatttatggataaaagaatcaaattctttatgttattcttttggttcttggggactacatattatttgatgaatgattttaatggtaaaacatttacag
|||| | || | |||||| ||| | | | |||||||||||||| ||||| ||||||||| |||| ||||| ||||||||||||| | | || | | || | || | | | || | | || || | | | | | | ||| ||
-GACAGGGGAGGCCTGTTCTAGATTGGTCGGCTAGGGTTAAAATTGCTGCAGGTGCTGCTCGTGGAATAGCGTATCTACATGAAGATTgtaatgctccttcctatttttgactatcttcacggtcattattccattatttcgacctaccttgtccctccacttatatctc-catttttcag------------------------------
upper sequence: AT1G26150.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM5G872442_T02 (Zea mays), 5'ss of exon 4
-CCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATTgtaggttgctacaactcttcaaaaatttatggataaaagaatcaaattctttatgttattcttttggttcttggggactacatattatttgatgaatgattttaatggtaaaacatttacag
|| ||| || | | | || ||| || | | ||||||||||| |||||| ||||||||||| |||| ||||| || |||||||||| ||| | || | || | | || ||| || || | | ||| | | | | | || | |
GACGT-GGAGTACCAGTTTTGGAGTGGCCAGCTAGGGTTAAAATTGCGGCTGGTTCGGCTCGTGGAATAGCCTATCTTCACGAAGATTgtaa----tgacatttttttcattcctttcacctgtttttgtgtgatgattttcactactcatgct-ctgttgcgtaattctt-ttcctcggcag---------------------------
upper sequence: AT1G26150.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G458548_T01 (Zea mays), 5'ss of exon 5
-CCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATTgtag-gttgctacaactcttcaaaaatttatggataaaagaatcaaattctttatgttattcttttggttcttggggactacatattatttgatgaatgattttaatggtaaaacatttacag
| | | | | | || |||| ||| | |||| |||||||||||||| ||||| ||||||||| | ||||| || || |||||||||| |||||| | || | ||| | || | | |||||| | | | | | |
GACACGGAATGCCTGTGT-TAGAATGGTCCGCACGGGTTAAAATTGCTGCAGGTGCTGCTCGTGGAATTGCTTACCTACACGAAGATTgtaatgttgcttc--ctacttctcgttttctttgcaatgttgttg---cttgcatgttaattgctgaacacatttgcag--------------------------------------------
upper sequence: AT1G26150.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G14310.1 (Glycine max), 5'ss of exon 3
CCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATTgtaggttgcta---caactcttcaaaaatttatggataaaagaatcaaattctttatgttattcttttggttcttggggactacatattatttgatgaatgattttaatggtaaaacatttacag
| ||| || | ||||| ||||||| |||||||||||||| |||||||| || || ||||||||||||||||||||||| |||| | | | | | || | ||| | | | | | || | ||| | | || | || | | | ||| || || | ||
GGGAAGGCCAGCCTGTGCTAGAATGGGCAAACCGTGTTAAAATTGCAGCTGGTGCAGCCCGAGGACTAGCTTATCTCCATGAAGACTgtaattaccaatccttattattttactctttgtcttgacatgcacataaatgcctat-cagtccactttccttttacgaaatttgaatttttgga--attggc----------------------
upper sequence: AT1G26150.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA01G23180.1 (Glycine max), 5'ss of exon 3
CCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATTgtaggttgctacaactcttcaaaaatttatggat---aaaagaatcaaattctttatgttattcttttggttcttggggactacatattatttgatgaatgattttaatggtaaaacatttacag
| ||| || | |||| ||||| | ||||| |||||||| |||||||| || || |||||| |||||||||||||||| |||| | | | | || | | ||| | | | | || | ||| ||| || ||| | | | || | ||
GGGAAGGTCAGCCTGTATTAGAATGGGCTAACCGTGTGAAAATTGCAGCTGGTGCAGCCCGAGGACTAACTTATCTCCATGAAGACTgtaattatcaatccttattattttactcttggtcttgacatgcacataaatgcctatcagtccactttcctttttgcaaatttgaatttttgcaattggc-------------------------
upper sequence: AT1G26150.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA16G19520.1 (Glycine max), 5'ss of exon 4
CCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATTgtaggttgctacaactcttcaaaaatttatggataaaagaatcaaattctttatgttattcttttggttcttggggactacatattatttgatgaatgattttaatggtaaaacatttacag
| ||| | || | || |||||| ||| ||||||||||||||| ||||| || || | ||| ||||||||||||||||||| |||| || ||| ||| | | ||| | | | | || ||| | || || || ||| | | || ||||| | | || ||| || |
GGGAAGGTAGGCCAGTGCTGGACTGGACAAAACGTGTTAAAATTGCGGCTGGGGCAGCCAGAGGAATAGCTTATCTCCATGAAGACTgtaa-ttat--caatccttaatatctttgttattgtga---------tgcttttgtaaggtcttgaatta--ggaaact-----tgaatttatgaagttggctgaaagtgaaaaatatg---
upper sequence: AT1G26150.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv01s0011g02460.t01 (Vitis vinifera), 5'ss of exon 3
CCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATTgtaggttgctacaactcttcaaaaatttatggataaaagaatcaaattctttatgttattcttttggttcttggggactacatattatttgatgaatgattttaatggtaaaacatttacag
| ||| | || | | | |||||||||||||||||||| ||||||||||||| ||||||||| |||||||||| |||||||| |||| || ||| | | | |||| ||||| | | | |||| | | | | | ||| ||||| | ||| | || |||| | | ||
GGGAAGGTAGGCCAGTTATGGACTGGGCAACACGTGTTAAGGTTGCTGCTGGTGCAGCTCGTGGAATAGCTTATCTTCATGAAGACTgtaagtatctatacttgtctcttcatttt--gataacaaagt------------attatccatctttgtgtagggtactaccaacctttttaaaaaaagc---aatgttcacctttt-----Mapped 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|47832052|gb|CK121736.1|CK121736EST: TAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATT GTCACCCTCGTATCATACATAGGGACATCAAATCATCCAACATTCTCTTAG
genomic: TAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATTgtaggttgct ... acatttacagGTCACCCTCGTATCATACATAGGGACATCAAATCATCCAACATTCTCTTAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CCGCAGGAACTCCGGGTCTAGACTGGGCAACACGTGTTAAAATTGCTGCTGGTGCGGCTCGTGGACTAGCTTATCTCCATGAAGATTgtaggttgctacaactcttcaaaaatttatggataaaagaatcaaattctttatgttattcttttggttcttggggactacatattatttgatgaatgattttaatggtaaaacatttacag
- - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA