Sequence
atgc intronic sequence ATGC exonic sequencegtaatgaccccactcttctttccaaaaagtagtctgcctgatcctgtctaaacagacccagttctttggttttttattttcatcttctcatatgctttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04930.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g20949.1 (Oryza sativa), 3'ss of exon 4
gtaatgaccccactcttctttccaaaaagtagtctgcctgatcctgtctaaacagaccc-agttctttggttttttattttcatcttc-tcatatgctttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG
||| | | | || | ||| | | | || ||| ||| ||| || ||| || | || || ||||||| |||||||| |||||||||||||||||||||||||| | || || || ||||||||||| | |||||||| |||||||| ||
----------------------------gtacagtttttttttctcgccaaatattcaggaattacttgatttactatatttttctcaatctgaaaagagGTACCTTTCCAGGTGCAAATGATGTATCCATGATTCAAATGGCTGATGTTGGTATTGGCATCAGTGGACAAGAAGGAAGGCAAGCTGTTATGGCATCAGA------------
upper sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g17010.1 (Oryza sativa), 3'ss of exon 4
gtaatgaccccactcttctttccaaaaagtagtctgcctgatcctgtctaaacagacccagttctttggttttttattttcatcttctcatatgctttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG
||| | ||| | | | | || | || | || | | ||| ||| || | | | || || | || || || |||| | ||||||| |||||||| || ||||||||||||||||||||||| || || || || || |||||||| || || ||||| |||||||| ||||| || |||||
gtattattccctcctggttctgc------tattatggcatataatattctgtgagaaccaatttatgtacatgtgat----atatgctaattaatcttttgttgtt-cagGTGCAAATGATGTTTCAATGATTCAAATGGCTGATGTTGGTGTTGGCATCAGTGGTCAAGAAGGACGGCAGGCTGTAATGGCATCAGATTTTGCGATGGG
upper sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G840699_T01 (Zea mays), 3'ss of exon 4
gtaatgaccccactcttctttccaaaaagtagtctgcctgatcctgtctaaacagacccagttctttggttttttattttcatcttctcatatgctttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG
||| | ||| | || ||| | | | || | | || || | | | | |||| | | ||| | || | || | ||| | ||| |||| || |||||||| || |||||||||||||||||||||||| | || || || || ||||||||||| |||||||| |||||||| ||||| | |||||
gtattattccctc-ctgcttctcttattatggtgtattttattctctatgatcttgatatgttca--aatctgatatatgaatttccttac---cttggcgtt----cagGCGCAAATGATGTTTCAATGATTCAAATGGCTGATGTTGGGATTGGCATCAGTGGCCAAGAAGGTCGACAAGCTGTTATGGCATCAGATTTTTCTATGGG
upper sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G407825_T01 (Zea mays), 3'ss of exon 4
gtaatgaccccactcttctttcc-aaaaagtagtctgcctgatcctgtctaaacagacccagttctttggttttttattttcatcttctcatatgctttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG
| | ||| | |||| |||| || | | | | | | ||| | || ||| | | | || ||||||| |||||||| |||||||||||||||||||| ||||| | || || || || ||||| || | |||||||| ||||| || ||||| || |||||
-----------attattccaacttaaaatgtaggacaaaggaagtagctcagaacttcatatatgttttatcttcacgagtcaaaaaatatgaaaacatacacgttttcagGTGCAAATGATGTATCCATGATTCAAATGGCTGACGTTGGCATCGGCATCAGTGGGCAAGAGGGAAGGCAAGCTGTTATGGCCTCAGATTTTGCCATGGG
upper sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 5
-------------gtaatgaccccactcttctttccaaaaagtagtctgc--ctgatcctgtctaaacagacccagttctttggttttttatttt---------catcttctcatatgc-tttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG
|| || | | | | | ||||| | | || || | | | | | | | | ||| | || | | ||| ||||| | ||| | |||||||| ||||||||||| ||||||||||||||||||||||| || || || || ||||||||||| || |||||||| |||||||||||||| ||||||||
gtaattgagttttgttataccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagaagtttttggctggtctgatttatgttctgaggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
upper sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G16040.1 (Glycine max), 3'ss of exon 4
---------------------gtaatgaccccactcttcttt-------ccaaaaagtagtctgcctgatcctgtctaaacagaccca-gttctttggttttttattttcatcttctcatatgctttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG
|| | ||| | ||| ||| || | | | | || || | || | ||||| |||| | || || || | ||| || || |||||||| ||||||||||| ||||| ||||||||||||||||| || || || || |||||||| ||||| |||||||| |||||||||||||| ||||||||
gtaattgatctgttagaccttgtggttccccttcaaaagtttgatagcattggaaaatattgagta-gtttttggctggtctgatttatgttctgtggtgtaataaatt--tcattatgcatgtgttacatt---acagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
upper sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G18580.1 (Glycine max), 3'ss of exon 7
--------------gtaatgaccccactcttctttccaaaaagtagtctgc--ctgatcctgtctaaacagacccagttctttggttttttatttt---------catcttctcatatgc-tttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG--
|| | | | | | | ||||| | | || || | | | | | | | ||| | || | | ||| ||||| | ||| | |||||||| ||||||||||| ||||||||||||| ||||||||| | || | || ||||||||||||| |||||||| |||||||||||||| ||||||||
gtaattgattttttgttagaccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCAGTGGACAAGAAGGTC--CAAGCTGTAATGGCATCTGATTTTGCAATGGGGC
upper sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------gtaatgaccccactcttctttccaaaaagtagtctgcctgatcctgtctaaa--cagacccagttctttggttttttattttcatcttctcatatgctttgtgtt-ttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG
| ||| | | | ||| || || | | || ||| | || | ||| ||||||||| | | ||| || | ||| | || ||||||| |||||||| || ||||| |||||||||||||| || | || || || || ||||| || || |||||||| |||||||| ||||| ||||||||
gtgagtattattcttccaatttatttaagactgataac-ttatgcttgcccaagaccaaaaaattagaagggaaaaaaaatctgatct-gttgtttggttttaggctaacg-cttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG
upper sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaatgaccccactcttctttccaaaaagtag----tctgcctgatcctgtctaaacagacccagttctttggttttttattttcatcttctcatatgctttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG
|| | || | | |||| | ||| | | | | || ||||| || | | || | | ||| | | ||| || |||| || || || || || ||||| ||||||||||||||||| || || || ||||| || ||||| || ||||| || ||||| |||||||| ||||||||
------------ttcgtgttactagtaagttgaagctcttcaaaacttcaggttctcttacatgtgtctttagtgcactttatta--catgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
upper sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ23939 (Selaginella moellendorffii), 3'ss of exon 5
gtaatgaccccactcttctttccaaaaagtagtctgcctgatcctgtctaaacagacccagttctttggttttttattttcatcttctcatatgctttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG
||| || || | | | || | | ||| || || | ||| |||||| ||||| || |||||||||| ||||| || || || || || ||||||||||||||||| || ||||| ||||||||||| ||||| ||||||
-----------------------------------------------gtaatcatctttgtttaggagatctcttgaataatttctctttaatctttaatcttt----agGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC
upper sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ21562 (Selaginella moellendorffii), 3'ss of exon 5
gtaatgaccccactcttctttccaaaaagtagtctgcctgatcctgtctaaacagacccagttctttggttttttattttcatcttctcatatgctttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG
||| || | ||| ||| | | | || | || |||| ||| |||||| ||||| || |||||||||| ||||| || || || || || ||||||||||||||||| || ||||| ||||||||||| ||||| ||||||
-----------------------------------------------gtaatcat-ctttgtttaggagttctcttgaataatttctctttaatctttaatcttt---agGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acccagttctttggttttttattttcatcttctcatatgctttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG
ttttttattttcatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgaccccactcttctttccaaaaagtagtctgcctgatcctgtctaaacagacccagttctttggttttttattttcatcttctcatatgctttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG