Sequence
atgc intronic sequence ATGC exonic sequencegtaagacttttcattctttcaggccttgtcactatactttccttatagctgcctactagtgaaatttgattgaattcctcaatgcagATGAAAGACTGAATGATATAGTTGGAAGTGCCTACTATGTCGCGCCTGAAGTTTTACACAGGTCATATAGCCTTGAGGCTGATATATGGAGTATTGGAGT
Basic information
| species | Arabidopsis thaliana |
| transcript | AT2G46700.2 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G46700.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g50030.1 (Oryza sativa), 3'ss of exon 5
--------gtaagacttttcattctttcaggccttgtcactatactttccttatagctgccta-----ctagtgaaatttgatt-gaattcctcaatgcagATGAAAGACTGAATGATATAGTTGGAAGTGCCTACTATGTCGCGCCTGAAGTTTTACACAGGTCATATAGCCTTGAGGCTGATATATGGAGTATTGGAGT
| | || ||| || | ||| || || | | |||||| | | || || | | || | | |||||||||||||| || |||||||| ||||||||||| || ||||| || || || ||||||||||| |||||||| | || || || || |||||||| || ||
ttaatgaactttggctaactatttttctcttcactgttgcttggtatttcat-tagctgaccagacaccttgttctttgtattttgtgctatataatgcagATGAAAGGCTTAATGATATTGTTGGAAGTGCATATTATGTTGCCCCAGAGGTTTTACACAGATCATATAGTATGGAAGCAGACATTTGGAGTATAGGTGT
upper sequence: AT2G46700.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os10g36710.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------------------------------gtaagacttttcattctttcaggcc---ttgtcactatactt--tccttatagctgcctac-tagtgaaatttgattgaattcctcaat-gcagATGAAAGACTGAATGATATAGTTGGAAGTGCCTACTATGTCGCGCCTGAAGTTTTACACAGGTCATATAGCCTTGAGGCTGATATATGGAGTATTGGAGT
|| | | | | || ||| | || | || | ||||| || | | || || | | ||| | | | || | ||||||||||| | |||||||| ||||| ||||| |||||||| || || ||||| |||| |||||||||||| || || || || ||||||||||| ||
gtatttccccccaaaagaattatgcccttccaaagaacttgtgtttcatcttatgttttttttttactctattatgaatttgtcctgacatggtgaaaatact-gttttttgaaaccaaatagtgaaaatactcaagtgttttgatgacacacatatttatgattggtcaatgccttcttttacagATGAAAGATTAAATGATATTGTTGGTAGTGCATACTATGTTGCTCCAGAAGTCCTACATAGGTCATATAGCACGGAAGCAGACATGTGGAGTATTGGTGT
upper sequence: AT2G46700.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G115518_T01 (Zea mays), 3'ss of exon 5
---gtaagacttttcattctttcaggccttgtcactatac--tttccttat-agctg--cctactagtgaaatttg-----attgaattcctcaatgcagATGAAAGACTGAATGATATAGTTGGAAGTGCCTACTATGTCGCGCCTGAAGTTTTACACAGGTCATATAGCCTTGAGGCTGATATATGGAGTATTGGAGT
| ||| | | || ||| | | | | | || || || | || || || | || |||| || | | ||||||||||||||| || |||||||| ||||||||||| || ||||| || || || ||| ||||||| ||||| || | || || || || |||||||| || ||
tggaatacactatcaacatttacagttaatattttttttcagttcactcattaactaaatcttatacttaattttgtgtgttctgcactatgcaatgcagATGAAAGGCTCAATGATATTGTTGGAAGTGCTTATTATGTTGCTCCAGAGGTTCTACACAGATCATACAGTATGGAAGCAGACATTTGGAGTATAGGTGT
upper sequence: AT2G46700.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G031893_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------gtaagacttttcattctttcaggccttgtcactata---ctttccttatagctgcctactagtga--aatttgattgaa------ttcctcaatgcagATGAAAGACTGAATGATATAGTTGGAAGTGCCTACTATGTCGCGCCTGAAGTTTTACACAGGTCATATAGCCTTGAGGCTGATATATGGAGTATTGGAGT
|| ||| | |||| | || ||| | ||||| | | ||| | || ||| | || | | |||||||||| || ||||| || ||||||||||| |||||||| || || ||||| || || |||||||||||| || || || || ||||| ||||| ||
gtattacatacctccgcacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtc-cattgacataaaatgaaacatgatatgaccttcctccaaaaaatgttctaacgcctgatgctcctgatgccttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGCATTGGTGT
upper sequence: AT2G46700.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G100560_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------gtaagacttttcattctttcaggccttgtcactata---ctttccttatagctgcctactagtg------aaatttgat--tgaattcctcaatgcagATGAAAGACTGAATGATATAGTTGGAAGTGCCTACTATGTCGCGCCTGAAGTTTTACACAGGTCATATAGCCTTGAGGCTGATATATGGAGTATTGGAGT
|| ||| | |||| | || ||| | ||||| | | ||| || |||| | | || | | |||||||||| || ||||| || ||||||||||| |||||||| || || ||||| || || |||||||||||| || || || || ||||| ||||| ||
gtattacatacctccacacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtc-cattgccataaaatgaaacatgatatgaccttcctccaaaaaatgttctaatgcctgatgctcctgatgctttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT
upper sequence: AT2G46700.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G138245_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------------gtaagacttttcat-tctttcaggccttgtcactatactttccttatagctgcctactagtgaaatttgattgaa-----ttcctcaatgcagATGAAAGACTGAATGATATAGTTGGAAGTGCCTACTATGTCGCGCCTGAAGTTTTACACAGGTCATATAGCCTTGAGGCTGATATATGGAGTATTGGAGT
||| | || | | | | || | | | || | || || | || || ||| ||| | |||||||||| || ||||| || ||||||||||| ||||| || || || ||||| || || |||||||||||| || || || || ||||||||||| ||
gtattacatacctccacacaaggatcatccattcctaatggagttctattttacaaatatgttagaagtccattgacataaaacgaaacatgatatgagcttcctctaaaagatgttttaaagcctgatgctcctgatgcctcctccccctcacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTACGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGTATTGGTGT
upper sequence: AT2G46700.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G173928_T01 (Zea mays), 3'ss of exon 5
--gtaagacttt-tcattcttt-----caggccttgtcactatactttccttatagctgcctactagtgaaatttg-----attgaattcctcaatgcagATGAAAGACTGAATGATATAGTTGGAAGTGCCTACTATGTCGCGCCTGAAGTTTTACACAGGTCATATAGCCTTGAGGCTGATATATGGAGTATTGGAGT
| ||||| | ||||| ||| | | || | | ||| ||| | || || | || || || | | | |||||||||||| || |||||||| |||||||| || || |||||||| || || ||| ||||||| || || || | || || || || |||||||| || ||
ttggaagacactatcattatttacagttaaccatttcttttgctcattcattaactcaatcttatacttaatcttatatgttctgtgctacatattgcagATGAAAGGCTCAATGATATTGTTGGAAGCGCATATTATGTCGCTCCAGAGGTTCTACACAGATCGTACAGTATGGAAGCAGACATTTGGAGTATAGGTGT
upper sequence: AT2G46700.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G05750.1 (Glycine max), 3'ss of exon 5
------gtaagactt-ttcattctttcaggccttgtcactatactt-tccttatagctgcctactagtgaaattt---gattgaattcctcaat--gcagATGAAAGACTGAATGATATAGTTGGAAGTGCCTACTATGTCGCGCCTGAAGTTTTACACAGGTCATATAGCCTTGAGGCTGATATATGGAGTATTGGAGT
|| | | |||| || | |||| ||| || | |||| | | | | || ||| | | | || ||||||| |||||||||| || ||||| ||||| || ||||| || ||||| || | |||||||||||||| || || || ||||||||||||||||| ||
tagtctgttccatgtactcataacccaagacattgttgggatatttatggatataaggccatccctcttaatttttcccttcatgtgtgttgatttacagATGAGCGACTGAATGACATTGTTGGGAGTGCGTATTATGTTGCACCTGAGGTCCTTCACAGGTCATATAGTCTGGAAGCAGATATATGGAGTATTGGTGT
upper sequence: AT2G46700.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G02340.1 (Glycine max), 3'ss of exon 6
------gtaagactt-ttcattctttcaggccttgtcactatactt-tccttatagctgcctactagtgaaattt---gattgaattcctcaat--gcagATGAAAGACTGAATGATATAGTTGGAAGTGCCTACTATGTCGCGCCTGAAGTTTTACACAGGTCATATAGCCTTGAGGCTGATATATGGAGTATTGGAGT
|| | | |||| || | |||| ||| || | |||| | | | | || ||| | | | | || |||||||| |||||||||| || || || ||||| || ||||| || ||||| || | |||||||||||||| || || || ||||||||||||||||| ||
tagtctgttccatgtactcataacccaagacattgttgggatatttatggatataaggtcatccctcttaatttttcccttcgtgtgtgttgatttacagATGAACGACTGAATGACATTGTCGGGAGTGCATATTATGTTGCACCTGAGGTCCTTCACAGGTCATATAGTCTGGAAGCAGATATATGGAGTATTGGTGT
upper sequence: AT2G46700.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv15s0048g02840.t01 (Vitis vinifera), 3'ss of exon 5
-----------------gtaagacttttcattctttcaggccttgtcactatactttccttatagctgcctactagtgaaatttgattgaattcctcaatgcagATGAAAGACTGAATGATATAGTTGGAAGTGCCTACTATGTCGCGCCTGAAGTTTTACACAGGTCATATAGCCTTGAGGCTGATATATGGAGTATTGGAGT
| || | | || ||| | | | | ||| |||| | | | | | || || | | |||||||||||||||| |||||||| ||||||||||| |||||||| || ||||||||| | || || || ||| || || || ||||| |||||| |||| ||
tcatttcataacttagcttgttacctatttccctctcaagtcaaa--atggaaattttcttac--ccgtttgtttttcccccttccaaatatgcatatatgcagATGAAAGACTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCTGAAGTTCTCCATAGATCCTATTATCTGGAAGCAGATATTTGGAGTGTTGGCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatactttccttatagctgcctactagtgaaatttgattgaattcctcaatgcagATGAAAGACTGAATGATATAGTTGGAAGTGCCTACTATGTCGCGCCTGAAGTTTTACACAGGTCATATAGCCTTGAGGCTGATATATGGAGTATTGGAGT
atttgat putative branch site (score: 5)
ttcctc putative PPT
aaatttgattgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagacttttcattctttcaggccttgtcactatactttccttatagctgcctactagtgaaatttgattgaattcctcaatgcagATGAAAGACTGAATGATATAGTTGGAAGTGCCTACTATGTCGCGCCTGAAGTTTTACACAGGTCATATAGCCTTGAGGCTGATATATGGAGTATTGGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
