Sequence
atgc intronic sequence ATGC exonic sequencegtttctttccatacacaccatagctacctttccttttcgaatgaaagattttggtcttgaaaatcgaatgttcgatgtcagGTTGAGCATCCTGTAACCGAGTGGATCGCCGAGGTTAATCTTCCTGCTGCTCAAGTTGCTGTTGGGATGGGAATTCCTCTCTGGCAAATCCCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G36180.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 3'ss of exon 10
gtttctttccat-acacaccatagctacctttccttttcgaatgaaagattttggtcttgaaaatcgaatgttcgatgtcagGTTGAGCATCCTGTAACCGAGTGGATCGCCGAGGTTAATCTTCCTGCTGCTCAAGTTGCTGTTGGGATGGGAATTCCTCTCTGGCAAATCCCTG
|| | | | ||| | || | | | | || | ||||| | || |||| || | ||||||||||||||||| || |||||||| || || || ||| | ||||| ||||||||||||||||| ||||| || || || ||||| || || |
gtcggctcctttgacattcttcaggaattaatttctgttgaccacatgatttacatt------gtcaaatggtc--tcacagGTTGAGCATCCTGTCACTGAGTGGATAGCTGAAGTAAATTTGCCTGCGGCTCAAGTTGCTGTTGGAATGGGTATACCCCTTTGGCAGATTCCAG
upper sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM5G858094_T02 (Zea mays), 3'ss of exon 8
gtttctttccatacacaccatagctacctttccttttcgaatgaaagattttggtcttgaaaatcgaatgttcgatgtcagGTTGAGCATCCTGTAACCGAGTGGATCGCCGAGGTTAATCTTCCTGCTGCTCAAGTTGCTGTTGGGATGGGAATTCCTCTCTGGCAAATCCCTG
|||| | | | || |||| | || | | | |||| ||| || |||| || ||| ||| |||||||||||||| || ||||||||||| || || || ||||| ||||| ||||||||||||||||| ||||| || ||||| ||||| || || |
gtttgctact-tgaactccattgactagttaatatgtaggg-gaaatcctttacaattttaaatt--atcttc-atg-cagGTTGAGCATCCAGTCACCGAGTGGATAGCTGAAGTAAATCTGCCTGCAGCTCAAGTTGCTGTTGGAATGGGCATACCTCTTTGGCAGATTCCAG
upper sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: AC197672.3_FGT002 (Zea mays), 3'ss of exon 8
gtttctttccatacacaccat-agctacctttccttttcgaatgaaagattttggtcttgaaaatcgaatgttcgatgtcagGTTGAGCATCCTGTAACCGAGTGGATCGCCGAGGTTAATCTTCCTGCTGCTCAAGTTGCTGTTGGGATGGGAATTCCTCTCTGGCAAATCCCTG
|||| | | | ||| ||| ||| ||| | | || || || |||| || ||| |||||||||||||| || || |||||||| || || || ||||| ||||| ||||||||||| ||||| ||||| || ||||| ||||| || || |
gtttgctact-tgaacatcattgactaataaacctgct---gcggaatccttcaaaattttaaattat---ctccatg-cagGTTGAGCATCCAGTCACTGAGTGGATAGCTGAAGTAAATCTGCCTGCAGCTCAAGTTGCAGTTGGAATGGGCATACCTCTTTGGCAGATTCCAG
upper sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 6
----------------------gtttctttccatacacaccatagctacctttccttttcgaatgaaagattttggtcttgaaaatcgaatgttcgatgtcagGTTGAGCATCCTGTAACCGAGTGGATCGCCGAGGTTAATCTTCCTGCTGCTCAAGTTGCTGTTGGGATGGGAATTCCTCTCTGGCAAATCCCTG
|| ||| | | | | | || |||| | || ||| | | | || || |||| || ||||||| |||||||| || |||||||| || ||| | ||||| || || || |||||||| |||||||||| || |||||||||||||| ||||
cttcctgttttatagaccctattttgttttttaatgttatttcatttttcctttatttttcaccatcagtgattgttttgctatattgattgttatat---agGTTGAACATCCTGTTACTGAGTGGATAGCAGAGATAAATCTGCCAGCAGCACAAGTTGCCATTGGGATGGGTATCCCTCTCTGGCAAATTCCTG
upper sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 6
-----------------------gtttctttccatacacaccatagctacctttccttttcgaatgaaagattttggtcttgaaaatcgaatgttcgatgtcagGTTGAGCATCCTGTAACCGAGTGGATCGCCGAGGTTAATCTTCCTGCTGCTCAAGTTGCTGTTGGGATGGGAATTCCTCTCTGGCAAATCCCTG
|||| ||| | | ||| | | || ||| || || ||| | | | || || |||| || ||||||| |||||||| || |||||||| || ||| | ||||| || || || |||||||| |||||||||| |||||||||||||||| ||||
tcccgttttccagaccctgttttgtttttttatgt-tatttcatttttcctttatttttgacaacatcagtgattgttttgctatattgattgttatat---agGTTGAACATCCTGTTACTGAGTGGATAGCAGAGATAAATCTGCCAGCAGCACAAGTTGCCATTGGGATGGGTGTTCCTCTCTGGCAAATTCCTG
upper sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 7
-------------gtttctttccatacacaccatagctacctttccttt---tcgaatgaaagattttggtcttgaaaatc--gaatgttcgatgtca-gGTTGAGCATCCTGTAACCGAGTGGATCGCCGAGGTTAATCTTCCTGCTGCTCAAGTTGCTGTTGGGATGGGAATTCCTCTCTGGCAAATCCCTG
| ||| || | ||||| | || | | | ||| | | | | || || || | | | | ||| ||| ||||| ||||| || |||||||| || || || ||||| || || || |||||||| || || ||||| ||||||||||||||||| ||||
tggttctgatacacgtcatttttatcagtgcaatagccaatttgcacctatgttagatgccatgtaatctttttaaatttcttaattaatttttatcaagGTGGAGCACCCTGTCACGGAGTGGATAGCAGAAGTAAATCTGCCAGCAGCCCAAGTTGCAGTAGGAATGGGGATTCCTCTCTGGCAAATTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctttccttttcgaatgaaagattttggtcttgaaaatcgaatgttcgatgtcagGTTGAGCATCCTGTAACCGAGTGGATCGCCGAGGTTAATCTTCCTGCTGCTCAAGTTGCTGTTGGGATGGGAATTCCTCTCTGGCAAATCCCTG
aaagatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttctttccatacacaccatagctacctttccttttcgaatgaaagattttggtcttgaaaatcgaatgttcgatgtcagGTTGAGCATCCTGTAACCGAGTGGATCGCCGAGGTTAATCTTCCTGCTGCTCAAGTTGCTGTTGGGATGGGAATTCCTCTCTGGCAAATCCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT