Sequence
atgc intronic sequence ATGC exonic sequencegtcaccaacagtgagcttggatttgattatctgagagacaatctagccacggaaagtaattcttgctttattttctcctttcattattgattgtatgagtttattttggatgttttttctgagttagtttctgattgtacagAGTGTTGAGGAGCTCGTCTTGAGGGATTTCAATTATTGTGTGATTGATGAAGTTGATTCCATACTTATTGATGAAGCAAGGACTCCTCTCATTATCTCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01800.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G01800.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g21820.1 (Oryza sativa), 3'ss of exon 3
----gtcaccaacagtga-gcttggatttgattatctga--gagacaatctagccacggaaagtaat--tcttgctttattttctcctttcattattgattgtatgagtttattttggat-----gttttttctgagttagtttctgatt---gtacagAGTGTTGAGGAGCTCGTCTTGAGGGATTTCAATTATTGTGTGATTGATGAAGTTGATTCCATACTTATTGATGAAGCAAGGACTCCTCTCATTATCTCTG
| | ||| || | | | | |||| | | || | | | || || || || | || | | ||| ||| | || | || ||| | || | || | | | | | || | |||| |||||| ||||| ||| ||||| | || || ||||||||||| ||||||||||||||||| || |||||||||||||| || ||||| || || || |
gtatgctgtttcctttgatagttatttgttaatgcctgattgggcacattcgtctttgaagtgtcataatcacatttccctctccctgtccataggtgaaggagtgcagtgataacagattcacagattctgctaactgattcttcattttttttgcagACTGTTGATGAGCTTGTCCTGAGGAACTTTAACTATTGTGTGATAGATGAAGTTGATTCCATTCTCATTGATGAAGCAAGAACACCTCTTATAATATCAG
upper sequence: AT4G01800.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G27810.1 (Glycine max), 3'ss of exon 5
gtcaccaacagtgagcttggatttgattatctgagagacaatctagccacggaaagtaattcttgc-tttattttctcctttcattattgattgtatgagtttattttggatgttttttctgagttagtttctgattgtacagAGTGTTGAGGAGCTCGTCTTGAGGGATTTCAATTATTGTGTGATTGATGAAGTTGATTCCATACTTATTGATGAAGCAAGGACTCCTCTCATTATCTCTG
||| | || | || ||||||| |||| | | |||| ||| | || | | ||| || | | | | | || |||||||||||| || || || ||| | |||| ||||||||| ||| | |||||||| |||||||| || |||||||||||||| || || || || ||||| || |
-------------------------------------gtaatttttcctttaca--tatttcttgcatttaaaatatgctttttagatttttagtttttatccttttaatatcatgctgaactctgaactgtggaatgtacagAGTGTCGAAGATCTTGTCATAAGGGGTTTCAATTACTGTATCATTGATGAGGTTGATTCAATCCTTATTGATGAAGCTAGAACGCCGCTTATTATATCAG
upper sequence: AT4G01800.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G27810.1 (Glycine max), 3'ss of exon 4
gtcaccaacagtgagcttggatttgattatctgagagacaatctagccacggaaagtaattcttgctttattttctcctttcattattgattgtatgagtttattttggatgttttttctgagttagtttctgattgtacagAGTGTTGAGGAGCTCGTCTTGAGGGATTTCAATTATTGTGTGATTGATGAAGTTGATTCCATACTTATTGATGAAGCAAGGACTCCTCTCATTATCTCTG
||||| || ||||||||||| |||||||| ||||||||||||| ||||||||||
gtcactaatagtgagcttggttttgattacttgagagACAATCTTGCCACGGAAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
upper sequence: AT4G01800.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G01060.1 (Glycine max), 3'ss of exon 5
gtcaccaacagtgagcttggatttgattatctgagagacaatctagccacggaaagtaattcttgctttattttctcctttcattattgattgtatgagtttattttggatgttttttctgagttagtttctgattgtacagAGTGTTGAGGAGCTCGTCTTGAGGGATTTCAATTATTGTGTGATTGATGAAGTTGATTCCATACTTATTGATGAAGCAAGGACTCCTCTCATTATCTCTG
|| |||| | || || || || ||| |||| ||| | ||| | || | || | || | || ||| || | || ||| | || ||| | |||| | | || | ||| | | | | | | || | | | ||
-------------------------------gtgtcgaagatcttgtcataaggggtttcaattactgtat----------cattgatga--ggttgattcaatccttattgatgaagctagAACA-CCGCTTATTATATCTGGACCTGCAGAGAAACCC---AGTGATC---AATATTATAAGGCTGCAAAGATTG--CAGAAGCCTTTGAACAAGACATACATTACACT-----------
upper sequence: AT4G01800.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 3'ss of exon 5
gtcaccaacagtgagcttggatttgattatctgagagacaatctagccacggaaagtaattcttgctttattttctcctttcattattgattgtatgagtttattttggatgttttttctgagttagtttctgattgtacagAGTGTTGAGGAGCTCGTCTTGAGGGATTTCAATTATTGTGTGATTGATGAAGTTGATTCCATACTTATTGATGAAGCAAGGACTCCTCTCATTATCTCTG
| || ||| ||| | | || | |||||| || | || | | ||| || | | || | | | || | || | | | | | || || | | ||| |||| | | || || | |
------------------------gcttgtctt-gaggggtttcaattactg--tgtaattgatgaggttgactcaattctgattgacgaa-gCAAGAACTCCTCTCA----TTATCTCAGGACCTGCT-----------GAAAAGCCAAGTGATAGGTACTATAAAGCTGCAAAAATTGCCTTGGCCTTTGAGCGAGATCTGCATTA----------------------------------
upper sequence: AT4G01800.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S9_141V6.2 (Physcomitrella patens), 3'ss of exon 4
----gtcaccaacagtgagcttgg-atttgattatctgagagacaatctagccacggaaagtaattcttgctttattttct-cctttcattattgattgtat--gagtttattttggatgttttt--tctgagttagtttctgattgtacagAGTGTTGAGGAGCTCGTCTTGAGGGATTTCAATTATTGTGTGATTGATGAAGTTGATTCCATACTTATTGATGAAGCAAGGACTCCTCTCATTATCTCTG
||| | | |||| ||| | ||| || | | || | | || ||| | |||| | ||| | |||| ||| ||| || | | ||||| | | | | | | || || | | |||| |||||| | || ||| | | |||||| | ||| |||||||||||||||||||| || ||||| |||||||| | ||||| ||||| || || |
gtaagtctaaatttacaatcttgatgtttcaatatacaggaactcctttgttgacaatcatgactttaagctatgttttttgtcttgtagtattaattttatccgaatgtggtttggtttgctgaagctttattcacttgctattgatgcagAACAAAGAGGAGTTAGTGTTGCGTGGTTTCAACTTTTGCGTGATTGATGAAGTTGATTCTATCCTTATCGATGAAGCTCGCACTCCACTCATCATATCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattgtatgagtttattttggatgttttttctgagttagtttctgattgtacagAGTGTTGAGGAGCTCGTCTTGAGGGATTTCAATTATTGTGTGATTGATGAAGTTGATTCCATACTTATTGATGAAGCAAGGACTCCTCTCATTATCTCTG
ttctgat putative branch site (score: 3)
tatgagtttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcaccaacagtgagcttggatttgattatctgagagacaatctagccacggaaagtaattcttgctttattttctcctttcattattgattgtatgagtttattttggatgttttttctgagttagtttctgattgtacagAGTGTTGAGGAGCTCGTCTTGAGGGATTTCAATTATTGTGTGATTGATGAAGTTGATTCCATACTTATTGATGAAGCAAGGACTCCTCTCATTATCTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC