Sequence
atgc intronic sequence ATGC exonic sequencegtgaaccgcaattcttccatttacttcatgtacatatatcaactaatttctaactgtttgacaccctgcgtgccttcgtgtgcctcctgcagGTCGTAGTGGTTTCTGGAGAAACTGGATGTGGTAAAACAACACAGCTTCCTCAGTACATATTAGAATCTGAGATCGAGGCTGCCCGTGGAGCTACATGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G48650.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G48650.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 5
gtgaaccgcaattcttccatttacttcatgtacata-tatcaactaatttc-taactgtttgacaccctgcgtgcctt-cgtgtgcctcctg------cagGTCGTAGTGGTTTCTGGAGAAACTGGATGTGGTAAAACAACACAGCTTCCTCAGTACATATTAGAATCTGAGATCGAGGCTGCCCGTGGAGCTACATGCA
| | | || |||| | | | | || || || | |||| | || | ||| || ||||| || |||||| | || ||||| || || ||||| |||||||| || ||||| || || |||||||| ||||||||||| ||||| ||||| ||||| ||||| ||||
-atatttgtcagcatttaggctactcgacttgcttggtactaaaaggctttgttgttgttcggcaatgttagtggctaacgtgtcttgtttggttgagcagGTCATTGTAGTTTCAGGCGAGACTGGCTGTGGTAAGACGACACAACTACCACAGTACATTTTAGAATCTGAAATCGATGCTGCTCGTGGTGCTACGTGCA
upper sequence: AT1G48650.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G34180.1 (Glycine max), 3'ss of exon 5
---gtgaaccgcaattcttccatttacttcatgtacatatatcaactaatttctaactgtttgacaccc----tgcgtgccttcgtgtgcctc-ctgcagGTCGTAGTGGTTTCTGGAGAAACTGGATGTGGTAAAACAACACAGCTTCCTCAGTACATATTAGAATCTGAGATCGAGGCTGCCCGTGGAGCTACATGCA
| |||| | | || || | |||| ||| | | | | | | ||| || | |||||||||| || || || || |||||||| |||||||| || ||||| |||||||| |||||||||||||||||||| || ||||| ||||||||| ||| |
attttcttttgcaaatttatttcttgtcaagactatgagtctcaatatgtttgtgatgaatgaaaatttatattaagtggtatcataaatgaaattgcagGTCGTCGTTGTCTCAGGTGAAACTGGTTGTGGTAAGACCACACAACTTCCTCAATACATATTAGAATCTGAGATTGAAGCTGCACGTGGAGCTGTATGTA
upper sequence: AT1G48650.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G05480.1 (Glycine max), 3'ss of exon 5
gtgaaccgcaattcttccatttacttcatgtacatatatcaactaatttcta-actgtttgacaccctgcgt-----gccttcgtgtgc---ctcctgcagGTCGTAGTGGTTTCTGGAGAAACTGGATGTGGTAAAACAACACAGCTTCCTCAGTACATATTAGAATCTGAGATCGAGGCTGCCCGTGGAGCTACATGCA
| |||| | | ||| || | |||| ||| | ||| ||| | | | | || | |||||||||| || || || || |||||||| |||||||| || ||||| |||||||| ||||||||||||||||||| || || || ||||||||| ||| |
-tcttttgcaaatttattttttgtcaagactattagtctcaatatgtttgtgtgctgaatgataatttatattaaagggtatcataaatgaaaatttgcagGTCGTTGTTGTCTCAGGTGAAACTGGTTGTGGTAAGACCACACAACTTCCTCAATACATATTAGAATCTGAGACTGAAGCGGCACGTGGAGCTGTATGTA
upper sequence: AT1G48650.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv17s0000g03030.t01 (Vitis vinifera), 3'ss of exon 4
gtgaaccgcaattcttccatttacttc-atgtacatatatcaactaatt------tctaactgtttgacacc--ctgcgtgccttcgtgtgcctcctgcagGTCGTAGTGGTTTCTGGAGAAACTGGATGTGGTAAAACAACACAGCTTCCTCAGTACATATTAGAATCTGAGATCGAGGCTGCCCGTGGAGCTACATGCA
| | | | | | | || ||| |||| |||||| | | || | | | ||| | || | || || | | | ||||| || || || || || |||||||| |||||||| || ||||| || ||||||||||| |||||||||||||| || ||||| ||||||||| || |
-cagattacgactatgctagtttcttagatgttattatatctagtgatggtgatattttcttatttaaaactgatgggttgtgtttctattaatttcacagGTGGTTGTAGTCTCAGGTGAAACTGGTTGTGGTAAGACCACACAACTCCCTCAGTACATTTTAGAATCTGAGATTGAAGCTGCTCGTGGAGCTTTCTGTA
upper sequence: AT1G48650.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ13473 (Selaginella moellendorffii), 3'ss of exon 5
gtgaaccgcaattcttccatttacttcatgtacatatatcaactaatttctaactgtttgacaccctgcgtgccttcgtgtgcctcctgcagGTCGTAGTGGTTTCTGGAGAAACTGGATGTGGTAAAACAACACAGCTTCCTCAGTACATATTAGAATCTGAGATCGAGGCTGCCCGTGGAGCTACATGCA
|| | | ||| | | || || ||||| || ||| |||| |||||||| ||||||||||||||||| |||||||| || || || | || | ||||| ||||| | | | || | || || |
---------------------------------------------gttggaagttctttttgttgttaaagtttcaagaaattcttctacagGTTGTGGTGATTTCAGGAGAAACAGGATGTGGTAAAACAACTCAGCTTCCACAATATATTCTGGAGGCAGAGATTGAGGCAGGCAGAGGCGGTAGCTGTA
upper sequence: AT1G48650.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ19043 (Selaginella moellendorffii), 3'ss of exon 5
gtgaaccgcaattcttccatttacttcatgtacatatatcaactaatttctaactgtttgacaccctgcgtgccttc-gtgtgcctcctgcagGTCGTAGTGGTTTCTGGAGAAACTGGATGTGGTAAAACAACACAGCTTCCTCAGTACATATTAGAATCTGAGATCGAGGCTGCCCGTGGAGCTACATGCA
| | || |||| | | | || || || ||||| || ||| |||| |||||||| ||||||||||||||||| |||||||| || || || | || | ||||| ||||| | | | || | || || |
-----------------------------------------gttggaagtt--ctttttgttgttgttaaagtttcaagtaattcttctacagGTTGTGGTGATTTCAGGAGAAACAGGATGTGGTAAAACAACTCAGCTTCCACAATATATTCTGGAGGCAGAGATTGAGGCAGGCAGAGGCGGTAGCTGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcaactaatttctaactgtttgacaccctgcgtgccttcgtgtgcctcctgcagGTCGTAGTGGTTTCTGGAGAAACTGGATGTGGTAAAACAACACAGCTTCCTCAGTACATATTAGAATCTGAGATCGAGGCTGCCCGTGGAGCTACATGCA
tgcctcct CT-rich tract
taatttctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaaccgcaattcttccatttacttcatgtacatatatcaactaatttctaactgtttgacaccctgcgtgccttcgtgtgcctcctgcagGTCGTAGTGGTTTCTGGAGAAACTGGATGTGGTAAAACAACACAGCTTCCTCAGTACATATTAGAATCTGAGATCGAGGCTGCCCGTGGAGCTACATGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT