Sequence
atgc intronic sequence ATGC exonic sequencegtgagaatcaaattaagatttacatatatgttcttgatttcaaaattggaatatttccaacttttggttaatgtaaatgtttcagGAAAAGTAGCGGTTTTTCGAGAGGAGCTTCAATATATAGAGGTGTCACAAGGCATCATCAACAAGGTCGCTGGCAAGCAAGAATCGGCCGTGTCGCAGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G65510.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G317160_T01 (Zea mays), 3'ss of exon 6
gtgagaatcaaattaagatttacatatatgttcttgatttcaaaattggaatatttccaacttttggttaatgtaaatgtttcagGAAAAGTAGCGGTTTTTCGAGAGGAGCTTCAATATATAGAGGTGTCACAAGGCATCATCAACAAGGTCGCTGGCAAGCAAGAATCGGCCGTGTCGCAGGA----------------------------
|| ||| |||| ||| ||| || || | ||||| | || || | | || ||| ||||| || ||||| || |||||||| ||||||||||||||||| |||||
--------------------------------------------------------gtaagtttcagttacagtaggc-catcatgatcgatatc--ttttttggcagtcattttcactt---gatttgttgtcagGCACCACCAACATGGACGCTGGCAGGCAAGAATCGGCCGTGTTGCAGGGAACAAGGATCTGTATCTTGGAACTTTCG
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G02760.1 (Glycine max), 3'ss of exon 7
gtgagaatcaaattaagatttacatatatgttcttgatttcaaaattggaatatttccaacttttggttaatgtaaatgtttcagGAAAAGTAGCGGTTTTTCGAGAGGAGCTTCAATATATAGAGGTGTCACAAGGCATCATCAACAAGGTCGCTGGCAAGCAAGAATCGGCCGTGTCGCAGGA
| | | | |||| | | || |||| |||||| | || | || | || || | | || | | | |||| | | ||| | || | || |||| | | || | | | |
--gttagtaactttaaattatttattgatgtacttgatcctatgtttcta-tactcataatttgtatct--tgcagGCATCATCAACAGGGTAGGTGGCAAGCAAGAATTGGCCGTGTAGCTGGAA-----ACAAAGATTTATACTTGGGAACATTCG---------------------------
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 7
gtgagaatcaaattaagatttacatatatgttcttgatttcaaaattggaatatttccaacttttggttaatgtaaatgtttcagGAAAAGTAGCGGTTTTTCGAGAGGAGCTTCAATATATAGAGGTGTCACAAGGCATCATCAACAAGGTCGCTGGCAAGCAAGAATCGGCCGTGTCGCAGGA----------------------------
||| ||||| | | | || || | | | | || |||| | | | ||| | || | || ||||||||||||| ||| | |||||||||||||| |||||||| || |||
----------------------------------------------------gtttgaaacttcaaatcatttagcatattgatgcacttgatactgtgtttctatac---ttataatttgta----tcctgca-gGCATCATCAACAGGGTAGGTGGCAAGCAAGAATTGGCCGTGTAGCTGGAAACAAAGATCTTTACTTGGGAACATTCG
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G02760.1 (Glycine max), 3'ss of exon 6
gtgagaatcaaat-taagatttacatatatgttcttgatttcaaaattggaatatttccaacttttggttaatgtaaatgtttcagGAAAAGTAGCGGTTTTTCGAGAGGAGCTTCAATATATAGAGGTGTCACAAGGCATCATCAACAAGGTCGCTGGCAAGCAAGAATCGGCCGTGTCGCAGGA
|| | | | | | ||| | || | | | ||| | || | | | || || || | | | | || |||||||||||| ||||| || || |||||||| ||||| |||||||| |||||
gtttgcttgagttgtcctattaaaattctagcattgtacttctacatacgcagctactgaatattcggat--ttccattcttgcagGAAAAGTAGTGGTTTCTCCAGGGGAGCTTCCATATACAGAGGTGTTACAAG-------------------------------------------------
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 6
gtgagaatcaaattaagatttacatatatgttcttg-atttcaaaattggaatatttccaacttttggttaatgtaaatgtttcagGAAAAGTAGCGGTTTTTCGAGAGGAGCTTCAATATATAGAGGTGTCACAAGGCATCATCAACAAGGTCGCTGGCAAGCAAGAATCGGCCGTGTCGCAGGA
|| | | | | ||| || | | ||| | ||| | || | | | || ||||| | | | | | || |||||||||||| ||||| || || |||||||| ||||| |||||||| |||||
gtttgcttgacttgccccattaaatttttagcattgtacttctacatatgcagctactgaaaatttggat--tttcattcttgcagGAAAAGTAGTGGTTTCTCCAGGGGAGCTTCCATATACAGAGGTGTTACAAG-------------------------------------------------
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv00s0772g00020.t01 (Vitis vinifera), 3'ss of exon 5
gtgagaatcaaattaagatttacatatatgttcttgatttcaaaattggaatatttccaacttttggttaatgtaaatgtttcagGAAAA-GTAGCGGTTTTTCGAGAGGAGCTTCAATATATAGAGGTGTCACAAGGCATCATCAACAAGGTCGCTGGCAAGCAAGAATCGGCCGTGTCGCAGGA----------------------------
| || |||| ||| || | || | | || | | | ||| | || | | | || | || | || | | | ||| | |||| | | | || ||||||||||||||||||| ||||||||||| || || || || || |||
---------gtttgaacatttccattcatttgaagcatacaactttcggtgttgagtccattttcgacatattcttttccattaagactacatattagcttgttgtaa--agcgggcaagtataatgatcttgca-gGCATCATCAACAAGGTCGATGGCAAGCAAGGATAGGTCGAGTTGCTGGAAATAAAGACCTGTACCTGGGGACATTTG
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv00s1291g00010.t01 (Vitis vinifera), 3'ss of exon 5
----gtgagaatcaaattaagatttacatat-atgttcttgatttcaaaattgga-atatttccaacttttggttaatgtaaatgtttcagGAAAAGTAGCGGTTTTTCGAGAGGAGCTTCAATATATAGAGGTGTCACAAGGCATCATCAACAAGGTCGCTGGCAAGCAAGAATCGGCCGTGTCGCAGGA
| || | | || | | | | || | || ||| | | | | | ||||||| || | ||| ||||||||||||||| || ||||| || |||||||| || || || |||||||||||
gtataccataacccacctatctgtagtctgttgtatttgttatctcatccataaataaaaattgaacttttatttcttccaaaattttcagGAAAAGTAGTGGCTTTTCAAGGGGAGCTTCCATTTACAGGGGTGTCACAAG------------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttgatttcaaaattggaatatttccaacttttggttaatgtaaatgtttcagGAAAAGTAGCGGTTTTTCGAGAGGAGCTTCAATATATAGAGGTGTCACAAGGCATCATCAACAAGGTCGCTGGCAAGCAAGAATCGGCCGTGTCGCAGGA
ggttaat putative branch site (score: 4)
aaaattggaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaatcaaattaagatttacatatatgttcttgatttcaaaattggaatatttccaacttttggttaatgtaaatgtttcagGAAAAGTAGCGGTTTTTCGAGAGGAGCTTCAATATATAGAGGTGTCACAAGGCATCATCAACAAGGTCGCTGGCAAGCAAGAATCGGCCGTGTCGCAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA