Sequence
atgc intronic sequence ATGC exonic sequencegtaatgcttttgtgttctttctttcttgaaagcttgtcttaagtctaagcttctcatgtgattctctctgtgcagGTCTTAACAGGTGTGGGAAGAGTTGCAGGCTAAGATGGACGAACTACTTGAGACCAGACATCAAGAGAGGGAGATTCTCTCCGGACGAGGAACAGACTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10280.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10280.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g51799.1 (Oryza sativa), 3'ss of exon 1
---------------------------------gtaatgcttttgtgttctttctttcttgaaagcttgtcttaagtctaagcttctcatgtga--------ttctctctg-----tgcagGTCTTAACAGGTGTGGGAAGAGTTGCAGGCTAAGATGGACGAACTACTTGAGACCAGACATCAAGAGAGGGAGATTCTCTCCGGACGAGGAACAGACTAT
| || | |||| | | ||| | || || | | | || || | | | |||||| || ||||||||||| ||||| |||||||||||||||||||||||| |||| ||||||||||||||||| | ||| | | | |||| | | || ||
gtatgtgtacatgcacaacggatggcgtacgtagctttgatcttgtagctagcatcgatccaaatgcagctatagctcgatggccatggcgttgagttttccttttttttacatgttgcagGGCTGAACAGGTGTGGCAAGAGCTGCAGGCTAAGATGGACGAACTACCTGAGGCCAGACATCAAGAGAGGAAAGTTCACCTCTGCCGAGAAGGATACCAT
upper sequence: AT5G10280.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g11780.1 (Oryza sativa), 3'ss of exon 1
----gtaatgcttttgtgttctttctttcttgaaagcttgtcttaagtct---------aagcttctcatgtg-attctctctgtgcagGTCTTAACAGGTGTGGGAAGAGTTGCAGGCTAAGATGGACGAACTACTTGAGACCAGACATCAAGAGAGGGAGATTCTCTCCGGACGAGGAACAGACTAT
|| || | | | | ||| | | | ||| || ||| | ||| | | | | || | | | |||||| | ||||| ||||| ||||| ||||||||||||||||| ||||| ||| |||||||||||||||||||| ||||| | || || || || |||||
gtgcttacacctctctcatgcatgtcttccacagaacatgtattcagtttcttgtatagaagtcttacttccgtatattgtttttgcagGCTTGAACAGATGTGGTAAGAGCTGCAGGCTAAGATGGACCAACTATCTGAAACCAGACATCAAGAGAGGGAACTTCTCGCGTGAGGAAGAGCAAACTAT
upper sequence: AT5G10280.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G159547_T01 (Zea mays), 3'ss of exon 1
-----------------gtaatgcttttgtgttctttctttct-----tgaaagcttgtcttaagtctaagcttctcatgtgat---------------tctctctgt----gcagGTCTTAACAGGTGTGGGAAGAGTTGCAGGCTAAGATGGACGAACTACTTGAGACCAGACATCAAGAGAGGGAGATTCTCTCCGGACGAGGAACAGACTAT
|| || | |||| || ||| ||| | | ||| | | |||| || ||| ||| ||||| || ||||||||||| ||||| |||||||| |||||||| ||||||||||| ||||||||||||||||||| ||| | | ||| || |||||||| ||
gtacgtgactgccgggaacaaacctctccatttctctcggtctcggtgtgacgatgtaaaagaggtcgatcgcttccatgcgaaaatgtagctcatcgatctagttgttattgcagGGCTCAACAGGTGTGGCAAGAGCTGCAGGCTGAGATGGACCAACTACTTGAGGCCAGACATCAAGAGAGGGAAGTTCACCCAGGAGGAAGAACAGACCAT
upper sequence: AT5G10280.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv11s0078g00480.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------gtaatgcttttgtgttctttctttcttgaaagct---tgtcttaagtctaagc--------ttctcatgtgattctctctgtgcagGTCTTAACAGGTGTGGGAAGAGTTGCAGGCTAAGATGGACGAACTACTTGAGACCAGACATCAAGAGAGGGAGATTCTCTCCGGACGAGGAACAGACTAT
| | |||| || | | ||| | | | || ||||| || ||| |||| | | ||| | | |||||||||| || ||||||||||||||||| |||||||||| || || ||||| || || ||||||||||||| ||| |||| || || || |||| ||
gtacaattcacacaatgaatcttttttttttttttttttcctttttctttttttgggtatctatctgtctctagcaaaaggcatgggtgttcttaattttgtcttaatttacagGTCTTAATAGATGTGGGAAGAGTTGCAGATTAAGATGGACTAATTATTTGAGGCCTGATATCAAGAGAGGGAAATTTTCTCGAGAAGAAGAGGAGACAAT
upper sequence: AT5G10280.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0141g00100.t01 (Vitis vinifera), 3'ss of exon 1
-----------gtaatgcttttgtgttctttctttcttgaaagct---tgtcttaagtctaagc--------ttctcatgtgattctctctgtgcagGTCTTAACAGGTGTGGGAAGAGTTGCAGGCTAAGATGGACGAACTACTTGAGACCAGACATCAAGAGAGGGAGATTCTCTCCGGACGAGGAACAGACTAT
|||| | | ||| ||| | | | || |||| || ||| |||| | | ||| | | | |||||||||| || ||||||||||||||||| |||||||||| || || ||||| || || ||||||||||||| ||| |||| || || || |||| ||
gtacaattcacacaatgaatcccccctttttttttttgggtatctatctgtcactagcaaaaggcatgggtgttcttaattttgtctatatttacagGTCTTAATAGATGTGGGAAGAGTTGCAGATTAAGATGGACTAATTATTTGAGGCCTGATATCAAGAGAGGGAAATTTTCTCGAGAAGAAGAGGAGACAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttcttgaaagcttgtcttaagtctaagcttctcatgtgattctctctgtgcagGTCTTAACAGGTGTGGGAAGAGTTGCAGGCTAAGATGGACGAACTACTTGAGACCAGACATCAAGAGAGGGAGATTCTCTCCGGACGAGGAACAGACTAT
ttctctctgt CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgcttttgtgttctttctttcttgaaagcttgtcttaagtctaagcttctcatgtgattctctctgtgcagGTCTTAACAGGTGTGGGAAGAGTTGCAGGCTAAGATGGACGAACTACTTGAGACCAGACATCAAGAGAGGGAGATTCTCTCCGGACGAGGAACAGACTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT