Sequence
atgc intronic sequence ATGC exonic sequencegtttccttaatagatttgtttcaaggagatttatggttgattcaggttcctttctcagtgaaataaatcttcttcactatgttttgttcccctcatacagTTGCGTGGGCGAAGTGGCCGGCAAGGGGATCCTGGAAGTTCCCGATTCTTCCTTAGTCTTGAAGATAACATATTCCGCATTTTTGGTGGAGATCGGATTC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01800.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os01g21820.1 (Oryza sativa), 3'ss of exon 13
gtttccttaatagatttgtttcaaggagatttatggt---tgattcaggttcctttctcagtgaaataaatcttcttcactatgttttgttcccctcatacagTTGCGTGGGCGAAGTGGCCGGCAAGGGGATCCTGGAAGTTCCCGATTCTTCCTTAGTCTTGAAGATAACATATTCCGCATTTTTGGTGGAGATCGGATTC
||| ||| | | | || || || | | | | ||| | || || | | || || | ||||| | || || || | ||||| ||||||||| |||||||||||||||| || || || ||||| ||||||||||| ||||| |||||||| |||||||| || || |||| |
ctttgaactccagaacaactactaactttttgatagtgttttgcttatgacacttcccca-tggatca--tcccatttgatttgtttgcattatctggtatagCTCCGTGGTCGAAGTGGCAGGCAAGGGGATCCTGGGAGCTCTCGGTTCTTTCTTAGTCTTGAGGATAATATATTCCGAATTTTTGGAGGTGACAGGATAC
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA10G27810.1 (Glycine max), 3'ss of exon 15
-------------------------------------------------------------------------------------------gtttccttaatagatttgtttcaaggagatttatggttgattc-aggttcctttctcagtgaaataaatcttcttcacta------tgttttgttcccctcatacagTTGCGTGGGCGAAGTGGCCGGCAAGGGGATCCTGGAAGTTCCCGATTCTTCCTTAGTCTTGAAGATAACATATTCCGCATTTTTGGTGGAGATCGGATTC
| || || ||| | | | | || | || ||| | | | | | || |||||| | || | | | |||| | | |||| || ||||||| ||||||||| | ||||| ||||| ||||| ||||| || ||| | |||||||||||||||||||| || ||||||||||||||||| ||||
gttttctcttctttccttttccttgtaaggttgaaaggagggaaactgggatgtactggcttgtggccttggacatctgcatatctcctaccctcttctattattattgcagctataataactactgctgcttctaccactcctaccctgttaaataagtatttaaaattggaacatttttttttatcatccataaagCTGCGTGGTCGAAGTGGCAGACAAGGAGATCCAGGAAGCTCCCGCTTTTTCTTAAGTCTTGAAGATAACATATTTCGTATTTTTGGTGGAGATCGAATTC
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA02G01060.1 (Glycine max), 3'ss of exon 15
-------------------------------------------------------------------------------------------gtttccttaatagatttgtttcaaggagatttatggttgattcaggttc-ctttctcagtgaaataaatcttcttcactatgttttgttcccct----catacagTTGCGTGGGCGAAGTGGCCGGCAAGGGGATCCTGGAAGTTCCCGATTCTTCCTTAGTCTTGAAGATAACATATTCCGCATTTTTGGTGGAGATCGGATTC
| || || ||| | | | | || | | ||| | | | | | || |||||| | || | || || | | |||| || ||||||| ||||||||| | ||||| ||||| ||||| || || || ||| | |||||||||||||||||||| || ||||||||||||||||| ||||
gtttttttatctttccttttccttgtagggttgaaaggtgggaagccgggatgtaatggcttgtggccttggacatccacatatctcctaccctcttctattattcttgcagctataatagctactgctacttctaccactcctaccctgtcaaataagtatttaaagttggaactttttttcatcatccataaagCTGCGTGGTCGAAGTGGCAGACAAGGAGATCCGGGAAGCTCACGCTTTTTCTTAAGTCTTGAAGATAACATATTTCGTATTTTTGGTGGAGATCGAATTC
upper sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 3'ss of exon 15
------gtttccttaatagatttgtttcaa----ggagatttatggttgattcaggttcctttctcagtgaaataaatcttcttcactatgttt------tgttcccctcatacagTTGCGTGGGCGAAGTGGCCGGCAAGGGGATCCTGGAAGTTCCCGATTCTTCCTTAGTCTTGAAGATAACATATTCCGCATTTTTGGTGGAGATCGGATTC
||||| || || ||| ||| | | || | ||| | | | | | | | | | | | |||| || ||| | | | | ||||||||||||| ||||||||||| ||||||||||| ||||||||||| |||||||||||||||||||||||||| || || |||||||| ||||| | ||||
gtgaaagtttcatttttatttttattttagatttgaagtggtggatgtgagtaaaatcctataatt--ttactttagttttctcatctgtgtgtgtgtaatccttcatctgtacagTTGCGTGGTCGAAGTGGCCGCCAAGGGGATCCAGGAAGTTCCCGTTTCTTCCTTAGTCTTGAAGATAACATCTTTCGAATTTTTGGGGGAGACAGAATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcctttctcagtgaaataaatcttcttcactatgttttgttcccctcatacagTTGCGTGGGCGAAGTGGCCGGCAAGGGGATCCTGGAAGTTCCCGATTCTTCCTTAGTCTTGAAGATAACATATTCCGCATTTTTGGTGGAGATCGGATTC
tcttcttcactatgtt CT-rich tract
aaataaatcttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttccttaatagatttgtttcaaggagatttatggttgattcaggttcctttctcagtgaaataaatcttcttcactatgttttgttcccctcatacagTTGCGTGGGCGAAGTGGCCGGCAAGGGGATCCTGGAAGTTCCCGATTCTTCCTTAGTCTTGAAGATAACATATTCCGCATTTTTGGTGGAGATCGGATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC