Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatgcaaaaactttgtctacatttacgctcattgtttatgttgtttagtacgtgcaaatgattcaagttttgctcatctttgtggtgttgtcagAAATTAAGCATATTGCCAAGAACAGGAGGGGCATTGGGATTTACATACATTCCTCCTACTAGTGAAGACAGATATTTACTCTTCATTGATGAGCTGCTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G47060.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 10
-gtaaaatgcaaaaactttgtctacatttacgctcattgtttatgtt-gtttagtacgtgcaaatgattcaagttttgctcatctttgtggtgttgtcagAAATTAAGCATATTGCCAAGAACAGGAGGGGCATTGGGATTTACATACATTCCTCCTACTAGTGAAGACAGATATTTACTCTTCATTGATGAGCTGCTTG
| || |||| | | || | | | | | | ||||| || | | | | || || ||| ||| || | ||| |||||||| || ||||||||||| |||| || |||||||| |||||||||| ||||| || | ||||| |||||||| ||||| ||||||| |||| ||
gtttgaacgcaagcaact-atcgatagaacagtttaa-gaaaatgttcgtcttgggcttaca-----ttttagtgttgttctttttt------ccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACCCCTCCCACAACAGAAGATAGATATTTGCTCTTTGTTGATGAACTGCGTG
upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G163193_T03 (Zea mays), 3'ss of exon 9
gtaaaatgcaaaaactttgtctacatttacgc--tcattgtttatgttgtttagtacgtgcaaatgattcaagttttgctcatctttgtggtgttgtcagAAATTAAGCATATTGCCAAGAACAGGAGGGGCATTGGGATTTACATACATTCCTCCTACTAGTGAAGACAGATATTTACTCTTCATTGATGAGCTGCTTG
|| | | ||| || | | || | | | | | | | ||| | || | | || || |||||||| || ||||||||||| ||||||| ||||| || |||||||||| ||||| || | || || |||||||||||||| ||||||| || | ||
------------------gtttgaacttaagcaattactgatagaacaatctgagagaag-atgtaatttgacttactttttcaatgctgaatttaacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG
upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 11
---gtaaaatgcaaaaactttgtctacatttacgctcattgtttatgttgtttagtacgtgcaaatg---attcaagttttgctcatctttgtggtgttgtcagAAATTAAGCATATTGCCAAGAACAGGAGGGGCATTGGGATTTACATACATTCCTCCTACTAGTGAAGACAGATATTTACTCTTCATTGATGAGCTGCTTG
|| ||| |||| | |||| | || | || || | || || || | | | | | ||||| | || || |||| | | |||| ||||||| ||||||||||||| || |||||||||| ||||||||||| |||| |||||| || | ||| |||||||| || || |||||||||||| ||| ||
attgtgttatg-aaaatcattgttaagtttcttatttgtttattgt-ttattaagaagatctataaggatattcatgccttact-atctcgg-gatgttatcagAAACTAAGCATATTGCCTAGGTCAGGAGGGGCTTTGGGATTTACTTACACTCCTCCAACAAATGAGGACAGATACTTGCTTTTCATTGATGAGTTGCGTG
upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 11
--gtaaaatgcaaaaactttgtctacatttacgctcattgtttatgttgtttagtacgtgcaaatg---attcaagttttgctcatctttgtggtgttgtcagAAATTAAGCATATTGCCAAGAACAGGAGGGGCATTGGGATTTACATACATTCCTCCTACTAGTGAAGACAGATATTTACTCTTCATTGATGAGCTGCTTG
| | | | ||| | ||| | | || ||| | || || || | | | | | ||||| | || ||| |||| || |||| ||||||| ||||||||||||| || |||||||||| ||||||||||| |||| |||||| || | ||| |||||||| || || |||||||||||| ||| ||
ttggagcctacttgtgtattgaaaatcattaagtttcttatttgt-ttattaagaaaatctataaggatattcatgccttactc-tcttggta-tgttatcagAAACTAAGCATATTGCCTAGGTCAGGAGGGGCTTTGGGATTTACTTACACTCCTCCAACAAATGAGGACAGATACTTGCTTTTCATTGATGAGTTGCGTG
upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 10
gtaaaatgcaaaaactttgtctacatttacgct-cattgtttatgttgtttagtacgtgcaa-atgattcaagttttgctcatctttgtggtgttgtcagAAATTAAGCATATTGCCAAGAACAGGAGGGGCATTGGGATTTACATACATTCCTCCTACTAGTGAAGACAGATATTTACTCTTCATTGATGAGCTGCTTG
||| | | ||| | | || | | || | | || || | ||| | | |||||||| | ||||| ||| ||||||| |||| ||||||||||| |||||||||| ||||| ||||| || |||||||| || | ||| || ||||| || || || | |||||| ||| ||
gtatataagttgtatcttggaaatctctatgttgcacattattagtccttaaatactttaaggatgattcagtgccttaatatcttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG
upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA18G07280.1 (Glycine max), 3'ss of exon 10
gtaaaatgcaaaaactttgtctacatttacgct-cattgtttatgttgtttagtacgtgcaa-atgattcaagttttgctcatctttgtggtgttgtcagAAATTAAGCATATTGCCAAGAACAGGAGGGGCATTGGGATTTACATACATTCCTCCTACTAGTGAAGACAGATATTTACTCTTCATTGATGAGCTGCTTG
||| | | ||| | | || | | || | || || | ||| | | ||||||||| | || || ||| ||||||| |||| ||||||||||| |||||||||| ||||| ||||| || |||||||| || | ||| || ||||| || || || | |||||| ||| ||
gtatataagttgtatcttggaaatctctatgttgcacatcattagtccttaaatactttaaggatgattcaatgccttaatatgttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG
upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 10
--gtaaaatgcaaaaactttgtctacatttacgctcattg--tttatgttgttta-gtacgtgcaaatgattcaagttttgctcatctttgtggtgttgtcagAAATTAAGCATATTGCCAAGAACAGGAGGGGCATTGGGATTTACATACATTCCTCCTACTAGTGAAGACAGATATTTACTCTTCATTGATGAGCTGCTTG
|| ||| | | | | ||| | ||| | |||| | || ||| | ||| | ||| | | | ||| ||||| ||||| || ||||||||||||||| |||||||||||||||| |||||||| | |||||| || | ||| ||||||||||| || |||||||||||| | | ||
tactaggatgtgagtccatcacatgcatacatgctttgtcattttaaatcgtccgcgtaacattagatggtccaa-tgctatctgtatttt--gtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTG
upper sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S10_296V6.2 (Physcomitrella patens), 3'ss of exon 13
-----------------------------------------------------------------gtaaaatgcaaaaactttgtctacat-ttacgc-tcattgtttatgttg--------tttagtacgtgcaaatgattcaagttttgctcatctttgtggtgttgtcagAAATTAAGCATATTGCCAAGAACAGGAGGGGCATTGGGATTTACATACATTCCTCCTACTAGTGAAGACAGATATTTACTCTTCATTGATGAGCTGCTTG
| | || |||| | | | | ||| || | ||| || ||| || || | || | | | || | ||||| | | ||| |||||| ||||||| ||||||||||||||||| || ||||| || || ||||| || ||| | |||||| | | |||| ||| |||||||||| |
gtacaacctccttttagttcttggtttctttgtttcttgtattcagcgtcagctcctaaatccgtatttgaacaaatgacttcatttccctcttatgcatggttgagtaggttacctccaccttctttagccgtgaaatttctcaaatgtggtgttcttt-ttatcttg-cagAAACTAAGCATTTTGCCAAGAACAGGAGGAGCTTTGGGTTTCACGTACATCCCCCCTGGTGCTGAAGATCGTAACCTACTGTTCGTTGATGAGCTAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgtttagtacgtgcaaatgattcaagttttgctcatctttgtggtgttgtcagAAATTAAGCATATTGCCAAGAACAGGAGGGGCATTGGGATTTACATACATTCCTCCTACTAGTGAAGACAGATATTTACTCTTCATTGATGAGCTGCTTG
aaatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatgcaaaaactttgtctacatttacgctcattgtttatgttgtttagtacgtgcaaatgattcaagttttgctcatctttgtggtgttgtcagAAATTAAGCATATTGCCAAGAACAGGAGGGGCATTGGGATTTACATACATTCCTCCTACTAGTGAAGACAGATATTTACTCTTCATTGATGAGCTGCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT