Sequence
atgc intronic sequence ATGC exonic sequencegtgagtatttttcatgttataatcatttctgagccactttctttcctgagtttgttatcaaattactcctcttttgtgtttcagTTACATGCGTCCTGAAACTGCTCAAGGTATTTTTGTCAACTTTAAGGACTTGTACTATTACAATGGGAAGAAACTTCCTTTTGCCGCGGCTCAAATTGGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G29880.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g42560.1 (Oryza sativa), 3'ss of exon 2
---------------gtgagtattttt----catgttataatcatttctgagccactttctttcctgagtttgttatc-aaattactcctcttttgtgt-----ttcagTTACATGCGTCCTGAAACTGCTCAAGGTATTTTTGTCAACTTTAAGGACTTGTACTATTACAATGGGAAGAAACTTCCTTTTGCCGCGGCTCAAATTGGT
| | | ||||| || | || | || | || || | | | || | ||| | | |||||||| ||| || ||| | || ||||| || || ||||||||||||||||| |||||||||||||||||||| ||| | || || ||||| || || |||||||| ||
gtaagaatatcaatgttcactttttttaacccaagagattaatgttcactgtttaattctgttgttatgctgattggctgaatgtgttcaattttgtgtgaacaaacagGTATATGAGACCAGAAACAGCACAGGGTATTTTTGTCAACTTCAAGGACTTGTACTATTACAACGGGCAAAAGCTCCCTTTCGCAGCAGCTCAAATCGGG
upper sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G821551_T03 (Zea mays), 3'ss of exon 2
gtgagtatttttcatgttataatcatttctgagccactttctttcctgagtttgtta-tcaaattactcctcttttgtgtttc------agTTACATGCGTCCTGAAACTGCTCAAGGTATTTTTGTCAACTTTAAGGACTTGTACTATTACAATGGGAAGAAACTTCCTTTTGCCGCGGCTCAAATTGGT
||||| || | || || | |||| | | | | || ||| || ||| | | |||||||| | || || ||||| || || || || || ||||||||||| ||||| ||||| |||||||||||||||| | || || |||||||| || |||||||||||
gtgagaatatctcc-------attctctctgtggttatgttccttttgtgttgattggctaaaaaggttcaattttgtgtggcggaaatagGTATATGCGACCAGAGACCGCACAGGGTATTTTTGTAAACTTCAAGGATCTGTACTATTACAATGGCCAAAAGCTCCCTTTTGCAGCTGCTCAAATTGGG
upper sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0150g00150.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtatttttcatgttataatcatttctgagccactttctttcctgagtttgt-tatcaaattactcctcttttgtgtttcagTTACATGCGTCCTGAAACTGCTCAAGGTATTTTTGTCAACTTTAAGGACTTGTACTATTACAATGGGAAGAAACTTCCTTTTGCCGCGGCTCAAATTGGT
|| || |||| || || ||| || ||| | | | | | ||| || | || | || | ||| || ||||| |||||||| |||||||| || ||||| || |||||||||||||||||||| ||||| | || ||||| ||||| || |||||||| |||
gtaaggattta----atttctattgcttc--agttgtattcaatttagtataggcatgccaatttcttttgctcatctgatgcagGTATATGCGCCCTGAAACAGCTCAAGGAATATTTGTAAATTTTAAGGACTTGTACTATTATAATGGCAGCAAGCTTCCCTTTGCTGCAGCTCAAATCGGTMapped 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|116404822|gb|EG447414.1|EG447414EST: TTTAATTTGATGTTTCAAACATCCATTGGCCCATCTGGTTTGATTCCTGG TTACATGCGTCCTGAAACTGCTCAAGGTATTTTTGTCAACTTTAAGGACTT
genomic: TTTAATTTGATGTTTCAAACATCCATTGGCCCATCTGGTTTGATTCCTGGgtgagtattt ... tgtgtttcagTTACATGCGTCCTGAAACTGCTCAAGGTATTTTTGTCAACTTTAAGGACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagccactttctttcctgagtttgttatcaaattactcctcttttgtgtttcagTTACATGCGTCCTGAAACTGCTCAAGGTATTTTTGTCAACTTTAAGGACTTGTACTATTACAATGGGAAGAAACTTCCTTTTGCCGCGGCTCAAATTGGT
ctcctcttttgtgttt CT-rich tract
tttgttatcaaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtatttttcatgttataatcatttctgagccactttctttcctgagtttgttatcaaattactcctcttttgtgtttcagTTACATGCGTCCTGAAACTGCTCAAGGTATTTTTGTCAACTTTAAGGACTTGTACTATTACAATGGGAAGAAACTTCCTTTTGCCGCGGCTCAAATTGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA