Sequence
atgc intronic sequence ATGC exonic sequence...gttcatttattgtgttgtgaactgtgatggtgtcatggtcgttgtatgaatgatgcctggaagaaaagtttactgaaattaaccatcgacattccaacagGTATTTTGTACTAACAGCAAGTGACCTAGAGGAGTGGTACCAGAACCCTGAGTCCTTTCATCATGAGCAGGACATGATTCAGTGGACAGAGAAATTGAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08960.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08960.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G18530.1 (Glycine max), 3'ss of exon 7
--gttcatttattgtgttgtgaactgtgatggtgtcatggtcgttgtatgaatgatgcctggaagaaaagtttactgaaattaaccatcgacattccaacagGTATTTTGTACTAACAGCAAGTGACCTAGAGGAGTGGTACCAGAACCCTGAGTCCTTTCATCATGAGCAGGACATGATTCAGTGGACAGAGAAATTGAGG
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ttattcaactatatgattgtaatttgctttga-gacttagtgatatttctccttatgattatgcactctatt-accagactaatgcctttatctttcaacagGTATTTTGTTCTGACAGCAAGTGATTTGGAAGAGTGGTATCGTAACCCTGAGTCTTTTCACCATGAGCAGGATATGGTTCAGTGGACAGAAAAATTGAGG
upper sequence: AT3G08960.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G19490.1 (Glycine max), 3'ss of exon 8
--gttcatttattgtgttgtgaactgtgatggtgtcatggtcgttgtatgaatgatgcctggaagaaaagtttactgaaattaaccatcgacattccaacagGTATTTTGTACTAACAGCAAGTGACCTAGAGGAGTGGTACCAGAACCCTGAGTCCTTTCATCATGAGCAGGACATGATTCAGTGGACAGAGAAATTGAGG
|||| ||| |||| | || || | | | || | | | ||| | || || | | | | | || ||||||||||||||| || ||||||||||| | || |||||||| | ||||||||||| ||||| ||||||||||| ||| ||||||||||||| |||||||||
ttattcaactatatgattgtaatttgctttga-gacttagtgatatttctccttatgattatgcactctatt-accagactaatgtctttatctttcaacagGTATTTTGTTCTGACAGCAAGTGATTTGGAAGAGTGGTATCGTAACCCTGAGTCTTTTCACCATGAGCAGGATATGGTTCAGTGGACAGAAAAATTGAGG
upper sequence: AT3G08960.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G43420.1 (Glycine max), 3'ss of exon 7
--gttcatttattgtgttgtgaactgtgatgg--tgtcatggtcgttgtatgaatgatgcctggaagaaaagtttactgaaattaaccatcgacattccaacagGTATTTTGTACTAACAGCAAGTGACCTAGAGGAGTGGTACCAGAACCCTGAGTCCTTTCATCATGAGCAGGACATGATTCAGTGGACAGAGAAATTGAGG
|||| ||| |||| | || || | | || | || | ||||| || | | |||| | | | | | | || ||||||||||||||| || ||||||||||| | || |||||||| | ||||| ||||| ||||| ||||||||||| ||| ||||||||||||| |||||||||
ttattcaactatatgattgtaatttgctttgagatttagtgatatttctccttatgat-tatgcactcta---ttaccagactaatgcctttatctttcaacagGTATTTTGTTCTGACAGCAAGTGATTTGGAAGAGTGGTATCGTAACCCCGAGTCTTTTCACCATGAGCAGGATATGGTTCAGTGGACAGAAAAATTGAGG
upper sequence: AT3G08960.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0217g00060.t01 (Vitis vinifera), 3'ss of exon 7
gttcatttattgtgttgtgaactgtgatggtgtcatggtcgttgtatgaatgatgcctgg--------aagaaaagtttactgaaatta-accatcgacattccaacagGTATTTTGTACTAACAGCAAGTGACCTAGAGGAGTGGTACCAGAACCCTGAGTCCTTTCATCATGAGCAGGACATGATTCAGTGGACAGAGAAATTGAGG
||||| || | | || | ||| || | || || | ||||| || || ||| || | | || || ||| ||||||||||||||| || |||||||||| | ||||||||||||||||| |||||||| ||||||||||||||||| ||| ||||||||||||| ||||||||
--------gttgtgagagcgcctttaacagtattatg-tccctctacttttggttcctggtttttgaaaattaatttttgctagggcaatgctattgatatttcaacagGTATTTTGTTTTATCAGCAAGTGATTTGGAGGAGTGGTACCAGAATCCTGAGTCTTTTCATCATGAGCAGGATATGGTTCAGTGGACAGAAAAATTGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgaatgatgcctggaagaaaagtttactgaaattaaccatcgacattccaacagGTATTTTGTACTAACAGCAAGTGACCTAGAGGAGTGGTACCAGAACCCTGAGTCCTTTCATCATGAGCAGGACATGATTCAGTGGACAGAGAAATTGAGG
aattaac putative branch site (score: 2)
tttactgaaattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcatttattgtgttgtgaactgtgatggtgtcatggtcgttgtatgaatgatgcctggaagaaaagtttactgaaattaaccatcgacattccaacagGTATTTTGTACTAACAGCAAGTGACCTAGAGGAGTGGTACCAGAACCCTGAGTCCTTTCATCATGAGCAGGACATGATTCAGTGGACAGAGAAATTGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccatc