Sequence
atgc intronic sequence ATGC exonic sequence...tagttggtctgatgaaaatgactgaacagtcgaaatatttactaaattttaagcttatatgattttgaatctttaacttttattttgtgtgtgtgtgcagATGGTCAAAGATTGCCTCTCATCTACCAGGAAGAACTGATAATGAAATAAAGAACCATTGGAACACACACATAAAGAAAAAGCTAAGGAAAATGGGTATT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G16600.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G16600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G106558_T02 (Zea mays), 3'ss of exon 2
-------------------tagttggtctgatgaaaatga-ctgaacagtcgaaatattt---actaaat-tttaagcttatatgattttgaat--ctttaacttttattttgtgtgtgtgtgc-agATGGTCAAAGATTGCCTCTCATCTACCAGGAAGAACTGATAATGAAATAAAGAACCATTGGAACACACACATAAAGAAAAAGCTAAGGAAAATGGGTATT
|| || ||||||||| ||| | | ||| | | || || ||| | | || | || | |||| ||| || || | || || |||||||||||||| || || | |||||| |||| || || || || |||||||| |||||||| ||||| ||||| ||||| ||||| ||||| ||
gtgccatgcatgcattgcatacccccacttctgaaaatgaactgtgttctgtatctatcttagattacatatttgaaggaaaataagcttagttttctttttttttaatgttcttaaaaaatgttagGTGGTCAAAGATTGCGTCGCACATGCCAGGACGAACGGACAACGAGATTAAGAACCACTGGAACACCCACATCAAGAAGAAGCTCAGGAAGATGGGGATC
upper sequence: AT5G16600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G39530.1 (Glycine max), 3'ss of exon 2
---tagttggtctgatgaaaatgactgaacagtcga-aatatttactaaattttaagcttatatgattttgaatctttaacttttattttgtgtgtgtgtgcagATGGTCAAAGATTGCCTCTCATCTACCAGGAAGAACTGATAATGAAATAAAGAACCATTGGAACACACACATAAAGAAAAAGCTAAGGAAAATGGGTATT
| | | | | | | || | | ||| ||||| ||||| || || | | ||| | | ||||| | | | ||||||||| |||||||| |||||||| || ||||||||||||||||| ||||| |||||||||||||| ||||||||||||||||| | ||||||||| |||
tttctttcattttcgcgtgttttcttttgtaatcaatactatatacta---tttaatactactatatatcattttactaattgtcattttcctttt-tactcagATGGTCCAAGATTGCTTCTCATCTCCCTGGAAGAACTGATAATGAGATAAAAAACCATTGGAACACCCACATAAAGAAAAAGCTCAAGAAAATGGGCATT
upper sequence: AT5G16600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G41180.1 (Glycine max), 3'ss of exon 2
tagttggtctgatgaaaatgactgaacagtcgaaatatttactaaattttaagcttatatgattt--tga-atctttaacttttattttgtgtgtgtgtgcagATGGTCAAAGATTGCCTCTCATCTACCAGGAAGAACTGATAATGAAATAAAGAACCATTGGAACACACACATAAAGAAAAAGCTAAGGAAAATGGGTATT
| || | | | | ||||| | |||| | | | | || ||| ||| | || ||| || ||| ||| | ||| | | | | ||||||||| |||||||| |||||||| || ||||||||||||||||| ||||| || ||||||||||||||||||||||||||||| | ||||||||| |||
tttttcatgttttttta-tgacttttagattaaaat--tcggttagtcatactcttttattaattattgatatttttttcttgtcatttttttttttactcagATGGTCTAAGATTGCTTCTCATCTCCCTGGAAGAACTGATAATGAGATAAAAAATCATTGGAACACACACATAAAGAAAAAGCTCAAGAAAATGGGCATT
upper sequence: AT5G16600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G33620.1 (Glycine max), 3'ss of exon 2
tagttggtctgatgaaaatgactgaacagtcgaaatatt--tactaaattttaagcttata-tgattttgaatctttaacttttattttgtgtgtgtgtgcagATGGTCAAAGATTGCCTCTCATCTACCAGGAAGAACTGATAATGAAATAAAGAACCATTGGAACACACACATAAAGAAAAAGCTAAGGAAAATGGGTATT
| || || || ||| | || | || ||| | | | | | || | ||| || | | ||| ||| | | | ||||||||||| |||||||| |||||||| |||||||||||||||||||| || ||||| || |||||||| ||||||||||||||||| | ||||||||| |||
--cctagtatggaccttttgttggaatcatttttttaataataataattgtgattcctttactaattactgatatcttgtatttttttcctccct-tatgcagATGGTCTAAGATTGCTTCTCATCTCCCAGGAAGAACTGATAATGAGATCAAGAATCACTGGAACACCCACATAAAGAAAAAGCTCAAGAAAATGGGAATT
upper sequence: AT5G16600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G04580.1 (Glycine max), 3'ss of exon 2
--tagttggtctgatgaaaatgactgaacagtcgaaatatttactaaattttaagcttatatgattttgaatctttaacttttattttgtgtgtgtgtgcagATGGTCAAAGATTGCCTCTCATCTACCAGGAAGAACTGATAATGAAATAAAGAACCATTGGAACACACACATAAAGAAAAAGCTAAGGAAAATGGGTATT-
| || || ||| ||| | | || | ||| | | | | || | || ||| | | |||| | | ||||||||||| |||||||| |||||||| ||||||||||| |||||||| || ||||| || ||||| || ||||||||||||||||| | ||||||||| |||
agttatttttcctatgtaaacattcctagtatggacct-tttgttggaatc--atttttttcctttactaattacagatgtcctttttttccccttatgcagaTGGTCTAAGATTGCTTCTCATCTCCCAGGAAGAACCGATAATGAGATCAAGAATCACTGGAATACCCACATAAAGAAAAAGCTCAAGAAAATGGGAATTG
upper sequence: AT5G16600.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0006g00450.t01 (Vitis vinifera), 3'ss of exon 2
------tagttggtctgatgaaaatgactgaacagtcgaaatatttactaaattttaagcttatatgattttgaatctttaacttttattttgtgtgtgtgtgcagATGGTCAAAGATTGCCTCTCATCTACCAGGAAGAACTGATAATGAAATAAAGAACCATTGGAACACACACATAAAGAAAAAGCTAAGGAAAATGGGTATT
| || ||| ||||| | | | | | | || | ||||| | || | | ||| || ||| ||| || ||| | ||||||||||| |||||||| |||||||||||||||||||| ||||| ||||| |||||||||||||| || ||||| |||||||| || | || |||||||||
ttccttttttttgtccc-tgaaattaattccaaaac--atatccatgtgaaattcttcttcaattttaatttatatgtttg---ttttttcaacgtggatttgcagATGGTCCAAGATTGCTTCTCATCTACCAGGAAGAACCGATAACGAAATCAAGAACCATTGGAATACCCACATCAAGAAAAAACTTAAAAAGATGGGTATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttaagcttatatgattttgaatctttaacttttattttgtgtgtgtgtgcagATGGTCAAAGATTGCCTCTCATCTACCAGGAAGAACTGATAATGAAATAAAGAACCATTGGAACACACACATAAAGAAAAAGCTAAGGAAAATGGGTATT
ctttaac putative branch site (score: 3)
ttatatgattttgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagttggtctgatgaaaatgactgaacagtcgaaatatttactaaattttaagcttatatgattttgaatctttaacttttattttgtgtgtgtgtgcagATGGTCAAAGATTGCCTCTCATCTACCAGGAAGAACTGATAATGAAATAAAGAACCATTGGAACACACACATAAAGAAAAAGCTAAGGAAAATGGGTATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - -atgaaaa
- - - - - - - - - - - - - - - - - - - -tactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattttg