Sequence
atgc intronic sequence ATGC exonic sequencegtacaaagttacaccttatttcacttgtggctaaagttggttttaaaggtaggattgtgattagaatttttatcttattaagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63680.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63680.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os04g58110.1 (Oryza sativa), 3'ss of exon 2
-------------------gtacaaagttacaccttatttcacttgtggctaaagttggttttaaaggtaggattgtgattagaatttttatcttattaagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG
|| | || | | |||| | || | | | |||| | | || | | ||| |||| | | || ||||||| |||||||| || || | || ||||||||||| ||| | ||||| |||||||| ||||||||| | ||||||||||| ||||||||||| | |
ttcgtgatgatgataatacatatgaggtgcctggtaatttaccatgctggttatgttg-ctgtgcgtctaatttctttcttaactttttccttgtttttagGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG
upper sequence: AT5G63680.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 2
----------gtacaaagttacaccttatttcacttgtggctaaa----gttggttttaaa--ggtaggattg--tgattagaatttttatcttattaagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG
| | | | | | ||| ||| | | || ||| || | | | | |||| | | | || || | ||| |||||||||||||||| || || | || || |||||||| ||| | || |||||||| || ||||||||| | |||||||| || ||||||||||| | |
tgacgctacatttccacctggtaggctgttttactcctaaccgaattctgttaacttcacatggatctgatttccttaatgatatggttctgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG
upper sequence: AT5G63680.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G008714_T01 (Zea mays), 3'ss of exon 2
-------------------gtacaaagttacaccttatttcacttgtggctaaagttggttttaaaggtaggattgtgattagaatttttatcttattaagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG
| | | || | ||||| | ||| | | | | || | | | | | || | | ||| ||| ||||||| |||||||| || || | || || |||||||| ||| | || |||||||| || ||||||||| | ||||||||||| ||||||||||| | |
ttcatattacatcatgataatgtacatatagaacttatgat-cgtgttggttatgctgtcatggatctgattcctttcatgatatggtttccgctatgcagGTTGAAAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCTGTTG
upper sequence: AT5G63680.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G09310.1 (Glycine max), 3'ss of exon 2
-------------gtacaaagttacaccttatttcacttgtggctaaagttggttttaaaggtaggattgtgattagaatttt----tatcttatt--aagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG
|||| ||| || || || ||| | | | ||| || | | | ||||| ||| |||| ||||||||||| || || |||||||||||||| || || || |||| || ||||||||||||||||| || |||||||||||||| |||||||| || |||
tatattctttataacacaa-gttgcatgctagtttgtttggtttttttccatatgctgaagataccagttcttctctgattttatgctatgctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACTGATGCATTCATGGTGGCACGTGGTGATCTTGGAATGGAGATCCCAGTAG
upper sequence: AT5G63680.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G00870.2 (Glycine max), 3'ss of exon 2
--------------gtacaaagttacaccttatttcacttgtggctaaagtt----ggttttaaaggtaggattgtgattagaatttttatcttattaagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG
| | ||| | | || | ||| | | | || || || |||| ||| |||| || | | | ||||||||||| || ||||||||||||||||| || || || |||| || ||||||||||||||||| || || ||||||||||| |||||||| || | |
tagcagactagcttgatctgttttatagatcatctttcttctcgttcttgtctttcaattcagaaatcctgatttatatttgaatgattgtatgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACTGATGCATTCATGGTGGCACGAGGTGATCTTGGAATGGAGATCCCAGTTG
upper sequence: AT5G63680.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0071g01060.t01 (Vitis vinifera), 3'ss of exon 2
gtacaaagttac--accttatttcacttgtggctaaag---ttggttttaaaggtaggattgtgattagaatttttatct-------------tattaagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG
| || |||| | || | | | | | ||| ||| ||| |||| | ||||| | | | || |||||||||||||||| || || | || |||||||| || || ||||| ||||| | ||||||||||| || |||||||| || |||||||| || | |
atgagaaattactgagtttctgtggttcttcaaggagtgttttgcatttcttggtcactgaatgatatgtttttttctttgttgagctgaaaattttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG
upper sequence: AT5G63680.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0056g00190.t01 (Vitis vinifera), 3'ss of exon 2
-------------------gtacaaagttacaccttatttcacttgtggctaaagttggttttaaaggtaggattgtgattagaatttttatcttattaagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG
|| ||| | | | |||| | | || | | || | | | | | | || | ||||| |||||||| || || || | || || ||||| || ||||||| || ||| |||| |||||||| |||||||||||||| |||||||| || | |
gcttatttcatggttggttgtgcaatttgcttacatgtttctttgataaatatgtcatagcctcatggcatcttcctttctgtggctgtaattcc-tgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggctaaagttggttttaaaggtaggattgtgattagaatttttatcttattaagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG
ggctaaa putative branch site (score: 3)
tttttatctt putative PPT
attgtgattagaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaaagttacaccttatttcacttgtggctaaagttggttttaaaggtaggattgtgattagaatttttatcttattaagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT