Sequence
atgc intronic sequence ATGC exonic sequencegtaattctttgttcctctttcttatacatgactctgcttgtagtattttacttagaagactaaggatggaatgtttttttttttttttatgttgggctttaactagATCAGCGTCTCAACGATGTGGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTTCACAGATCCTATAGCACCGAAGCAGATATATGGAGCATTGGTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G49370.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G49370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os10g36710.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------gtaattctttgttcctctttcttatacatgactctgcttgt----agtattttacttagaagactaaggatggaa-tgtttttttttttt-------------tttatg-ttgggctttaact--------agATCAGCGTCTCAACGATGTGGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTTCACAGATCCTATAGCACCGAAGCAGATATATGGAGCATTGGTGT
| || ||| || |||| | | | || | | || | || | | || ||| | || || || | | | |||| |||||| |||| | | || |||| | | | || ||| | || || ||||||||||||||||| || ||||| || || || || |||||||| |||||||| || ||||| ||||||||
gtatttccccccaaaagaattatgcccttccaaagaacttgtgtttcatcttatgttttttttttactctattatgaatttgtcctgacatggtgaaaatactgttttttgaaaccaaatagtgaaaatactcaagtgttttgatgacacacatatttatgattggtcaatgccttcttttacagATGAAAGATTAAATGATATTGTTGGTAGTGCATACTATGTTGCTCCAGAAGTCCTACATAGGTCATATAGCACGGAAGCAGACATGTGGAGTATTGGTGT
upper sequence: AT3G49370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G031893_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------gtaattctttgttcctctttcttatacatgactctgcttgtagtattttacttagaagactaaggatggaatgttt--ttttttttttttatgttgggctttaactagATCAGCGTCTCAACGATGTGGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTTCACAGATCCTATAGCACCGAAGCAGATATATGGAGCATTGGTGT
|| | |||| | | | |||| | | ||| | | || | | || | | | | | | | || | || || |||| | | || || || | || |||||||||||||||||||| || ||||| | || || || |||||||| |||||||| || ||||||||||||||
gtattacatacctccgcacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgacataaaatgaaacatgatatgaccttcctccaaaaaatgttctaacgcctgatgctcctgatgccttttccccctttac-agATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGCATTGGTGT
upper sequence: AT3G49370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G100560_T01 (Zea mays), 3'ss of exon 5
----------------------------------gtaattctttgttcctctt-tcttatacatgactctgcttgtagtattttac-ttagaagact--------aaggatg---gaatgttttttttttttttta-tgttgggctttaactagATCAGCGTCTCAACGATGTGGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTTCACAGATCCTATAGCACCGAAGCAGATATATGGAGCATTGGTGT
|||| | |||| | | | || | | | | || || || | | | ||| || ||| |||| | | | | | | || | | |||| | | || || || | || |||||||||||||||||||| || ||||| | || || || |||||||| |||||||| || ||||| ||||||||
gtattacatacctccacacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgccataaaatgaaacatgatatgaccttcctccaaaaaatgttctaatgcctgatgctcctgatgctttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT
upper sequence: AT3G49370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G138245_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------------gtaattctttgttcctctttcttatacatgactctgcttgtagtattttacttagaagactaaggatggaatgtttttttttttttttatgttgggctttaactagATCAGCGTCTCAACGATGTGGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTTCACAGATCCTATAGCACCGAAGCAGATATATGGAGCATTGGTGT
|| | |||| | | | |||| | | | ||| | | | | | || | | | | | | | | |||| | | || || || | || |||||||||||||| ||||| || ||||| | || || || |||||||| |||||||| || ||||| ||||||||
gtattacatacctccacacaaggatcatccattcctaatggagttctattttacaaatatgttagaagtccattgacataaaacgaaacatgatatgagcttcctctaaaagatgttttaaagcctgatgctcctgatgcctcctccccctcacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTACGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGTATTGGTGT
upper sequence: AT3G49370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 5
gtaattctttgttcctctttcttatacatgactctgcttgtagtattt-tacttagaagactaaggatggaatgtttttttttttttttatgttgggctttaactagATCAGCGTCTCAACGATGTGGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTTCACAGATCCTATAGCACCGAAGCAGATATATGGAGCATTGGTGT
| ||| | | | |||| | | || ||| ||| | || | | | |||||| | | || | | |||| ||||||| |||||||| ||| | || ||||||||||||||||||||||| |||||||| ||||||||||| | ||||| ||| | ||||||||||| ||
-tgtttcaactccttagacaatcacctctctctctctctctcgtgtttgcactgattcatcttaagtttgaatgtaacagtcagctcttttat---gcttg---tagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagaagactaaggatggaatgtttttttttttttttatgttgggctttaactagATCAGCGTCTCAACGATGTGGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTTCACAGATCCTATAGCACCGAAGCAGATATATGGAGCATTGGTGT
atggaatgtttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattctttgttcctctttcttatacatgactctgcttgtagtattttacttagaagactaaggatggaatgtttttttttttttttatgttgggctttaactagATCAGCGTCTCAACGATGTGGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTTCACAGATCCTATAGCACCGAAGCAGATATATGGAGCATTGGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA