Sequence
atgc intronic sequence ATGC exonic sequence...tacggatttgtcgtgggaatgtgttaaatcaatgttttacatgttaacttgttagttttgtttcgcttcaatctgtctcacctatcatttgaatatgtagGAAGGGTTACGGTAAAATATCTGCATCGGGTGGGAGGGGATGGGGTGGAGGTGGCGGAGGAAGGATCTCTCTTGACTGTTACAGCATACAAGAAGATGTC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G47020.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os04g10380.1 (Oryza sativa), 3'ss of exon 1
tacggatttgtcgtgggaatgt-gttaaatcaatgttttacatgttaacttgttagttttgtttcgcttcaatctgtctcacctatcatttgaatatg-----tagGAAGGGTTACGGTAAAATATCTGCATCGGGTGGGAGGGGATGGGGTGGAGGTGGCGGAGGAAGGATCTCTCTTGACTGTTACAGCATACAAGAAGATGTC
|| | | ||| | | | |||||| | | | | || ||| | | || || | ||| ||| ||| | || | |||| ||| ||| | ||||| | ||||||||||||||||| || || ||||| ||||| |||||||||||||| || ||||| |
------cttcccctaggagttttactgaatcaaaccccatacttctgttctatgctttctgtggtgatctgtgagatccaactccttattctaatgccattcttagATATGGAAATGGTACGATAAGTGCTGCTGGTGGTAATGGATGGGGTGGAGGTGGTGGTGGGAGGATATCTCTGGACTGTTACAGCATTCAGCAAGATCTG
upper sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G385413_T01 (Zea mays), 3'ss of exon 1
tacggatttgtcgtgggaatgtgttaaatcaatgttttac---atgtta-acttgttagttttgtttcgcttcaatctgtctcacct-atcatttga-atatgtagGAAGGGTTACGGTAAAATATCTGCATCGGGTGGGAGGGGATGGGGTGGAGGTGGCGGAGGAAGGATCTCTCTTGACTGTTACAGCATACAAGAAGATGTC
| | |||| | ||| || ||| ||| || | || || ||| || | | | ||||| || | | || || || ||| || | || | |||| ||| | ||||| | ||||||||||| |||||||| |||||||| ||||| |||||||||||||| ||| ||||| |
-----ttccccccctggaaagacacaaacaaaccccataccctatgctacatttttttgttgtgacttg-tgaaatctaactgtcatcatggcatgccattcttagATCTGGAAATGGCACAATAAGTGCTGCTGGTGGTAATGGATGGGGTGGCGGTGGCGGTGGAAGGATATCTCTGGACTGTTACAGCATTCAACAAGATTTG
upper sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G41140.1 (Glycine max), 3'ss of exon 1
---tacggatttgtcgtgggaatgtgttaaatcaatgttttacatgttaacttgttagttttgtttcgcttcaatctgtctcacct-atcatttgaata--tgtagGAAGGGTTACGGTAAAATATCTGCATCGGGTGGGAGGGGATGGGGTGGAGGTGGCGGAGGAAGGATCTCTCTTGACTGTTACAGCATACAAGAAGATGTC
| | || ||| ||| || || | | | ||||| || || || | || || || ||| | || | || |||| | ||||||||||| || |||| || ||| | ||||||| ||||||||||||||| || |||||||| || || ||||| |||||||||||||||||||
aagtgcc-atgtgtatgttgaaggttttgtagggaactaatacatattgtctagtgaattgtgcttgtaacttttcttttcaacttcattttttggttgagTGTAGGAAGGGCTATGGTATCATCAGTGCCGCTGGTGGGACGGGATGGGGTGGAGGAGGTGGAGGAAGAATATCACTTGATTGTTACAGCATACAAGAAG-----
upper sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G04290.1 (Glycine max), 3'ss of exon 1
tacggatttgtcgtgggaatgtgttaaatcaatgttttacatgttaacttgttagttttgtttcgcttcaatctgtctcacct-atcatttgaata--tgtagGAAGGGTTACGGTAAAATATCTGCATCGGGTGGGAGGGGATGGGGTGGAGGTGGCGGAGGAAGGATCTCTCTTGACTGTTACAGCATACAAGAAGATGTC
|| ||| ||| || || || | | ||||| ||| | || | || || || ||| | || | || || | | ||||||||||| || |||| || ||| | ||||| | ||||||||||||||| || |||||||| || || ||||| ||||||||||||||||||||| |
---ccatgtgtacattgaaggttttgtatggaactaatacatattatccagtgaattgtgcttgtaacttttcttttcaacttcatttttcggttgagtgtagGAAGGGATATGGTATCATCAATGCTGCTGGTGGAATGGGATGGGGTGGAGGAGGTGGAGGAAGAATATCACTTGATTGTTACAGCATACAAGAAGATTTT
upper sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0012g00460.t01 (Vitis vinifera), 3'ss of exon 1
-tacggatttgtcgtgg-gaatgtgttaaatcaatgttttacatgttaacttgttagttttgtttcgcttcaatctgtctcacctatcatttgaatatgtagGAAGGGTTACGGTAAAATATCTGCATCGGGTGGGAGGGGATGGGGTGGAGGTGGCGGAGGAAGGATCTCTCTTGACTGTTACAGCATACAAGAAGATGTC
| | | || ||| ||| | | ||| | | || |||| | | |||| | || || | | ||||||| | ||||||||| || || | ||| |||| | ||||| || ||||||||||||||||| || ||||| || || || || ||||| ||||||||||||||||||
agatgttgcgtccatgacaaattaattatgtaattgtaatcta-gtggactttctgtggatttttctccctaa-ctatttacttaatcatttatttggatagGAAGGGATATGGCACTATAAGTGCAGCAGGTGGTAGTGGATGGGGTGGAGGTGGAGGTGGAAGAATATCACTGGATTGTTATAGCATACAAGAAGATGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacttgttagttttgtttcgcttcaatctgtctcacctatcatttgaatatgtagGAAGGGTTACGGTAAAATATCTGCATCGGGTGGGAGGGGATGGGGTGGAGGTGGCGGAGGAAGGATCTCTCTTGACTGTTACAGCATACAAGAAGATGTC
tatcatttgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacggatttgtcgtgggaatgtgttaaatcaatgttttacatgttaacttgttagttttgtttcgcttcaatctgtctcacctatcatttgaatatgtagGAAGGGTTACGGTAAAATATCTGCATCGGGTGGGAGGGGATGGGGTGGAGGTGGCGGAGGAAGGATCTCTCTTGACTGTTACAGCATACAAGAAGATGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - gatttgt
- - - - - - - - - - - - -aaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaccta