Sequence
atgc intronic sequence ATGC exonic sequencegtgatcatcttaatgaataatcttattactgtttggtatataagcactcatgtaaggaaagaaattgtagctgatatgaaattgataagatctgtacctctgtattagGCAGCAAATCCTGGCTGTATTTTGGAAGATTTTGTGAGATGGCACTCGCCACCAGACTGGACTGAAAATGGTAACATGTCTGGAGATGACTCTTCACCCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55060.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G55060.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G076387_T01 (Zea mays), 3'ss of exon 8
gtgatcatcttaatgaataatcttattactgtttggtatataagcactcatgtaaggaaagaaattgtagctgatatgaaattgataa--gatctgtacctctgt-atta--gGCAGCAAATCCTGGCTGTATTTTGGAAGATTTTGTGAGATGGCACTCGCCACCAGACTGGACTGAAAATGGTAACATGTCTGGAGATGACTCTTCACCCG------
|| || | || | | || || | | || | | |||| || ||| | | | || | | |||| ||||||||||||||| ||| | ||||||| ||||| ||||||||||| ||||| || ||| |||| || || ||| | | | || |
-------------------------------gcaagtttaaagctgttcttctcagagaatacaatgctattaaactgaacttcctaaacaagcaatttctttttcattacagGCAGCAAATCCTGGTTGTGTCCTGGAAGACTTTGTTAGATGGCACTCTCCACCCGATTGGTCTGAGGATTGTG------CTGCAAACAGTACCACAGTTGGGGAAG
upper sequence: AT5G55060.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G10700.1 (Glycine max), 3'ss of exon 3
----gtgatcatcttaatgaataatcttattactgtttggtatataagcactcatgtaaggaaagaaattgtagctgatatgaaattga--taagatctgtacctctgtattagGCAGCAAATCCTGGCTGTATTTTGGAAGATTTTGTGAGATGGCACTCGCCACCAGACTGGACTGAAAATGGTAACATGTCTGGAGATGACTCTTCACCCG
| | ||| | || | | || |||||| | | | | || || || | | ||| |||| |||| | | | | | ||| ||| |||||| ||||||||||| || |||||||||||||||||||||||| ||||||| || || |||| |||| || | ||| ||| |||
gtcagattttcccttgaagagaacttttcttactgatat---tcttaatgcttttgaaatgcatctaat-gtag-tgatgttctctctaagttctgtttgtggtcatgttttagGCTGCAAATCCTGGTTGCATTTTGGAAGATTTTGTGAGATGGTACTCGCCTCCTGATTGGATGGAAAGTGAGGGAAGTACTGAAGACAGAGATTCTTTTT
upper sequence: AT5G55060.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G43140.1 (Glycine max), 3'ss of exon 8
----gtgatcatcttaatgaataatcttattactgtttggtatataagcactc----atgtaaggaaagaaattgtagctgatatgaaattgataagatctgtacctctgtattagGCAGCAAATCCTGGCTGTATTTTGGAAGATTTTGTGAGATGGCACTCGCCACCAGACTGGACTGAAAATGGTAACATGTCTGGAGATGACTCTTCACCCG
| | ||| | || | | || |||||| | | ||| | ||| | || | | | | || | | | | | | | || | || |||||| ||||||||||| || |||||||||||||||||||||||| |||| || || || |||| ||||| || | ||| ||| ||| |
gtcagattttcccttgaagagaacttttcttactgat--attcttaattcttttggaatgcatctaatgtagtgatgctctatctaagttagttctgttttgc-ctcatgatttagGCTGCAAATCCTGGTTGCATTTTGGAAGATTTTGTGAGATGGTACTCTCCTCCTGATTGGAGTGAAAGTGAGGGAAGTACTGAGGATAGAGATTCTTCTT
upper sequence: AT5G55060.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA14G02550.1 (Glycine max), 3'ss of exon 9
----gtgatcatcttaatgaataatcttattactgtt-tggtatataagcactcatgtaaggaaagaaattgtagctgatatgaaattgataagatctgtacctctgtattagGCAGCAAATCCTGGCTGTATTTTGGAAGATTTTGTGAGATGGCACTCGCCACCAGACTGGACTGAAAATGGTAACATGT-CTGGAGATGACTCTTCACCCG
| | ||| | | | | | |||||| | | || || | | | ||| | | | | | || | | ||| | | |||||| ||||||||||| ||||||||||| |||||||| ||||||||||| || || || ||||| || |||| | || || | | ||| | |
gtaaggggctcccttgaagggaacttctcttactgatattgtgaatgcttcttactatgttgaatgtgcctaatgttctgtctgagttagttttgtttgttatcatattttagGCTGCAAATCCTGGATGTATTTTGGAGGATTTTGTAAGATGGCACTCTCCTCCTGATTGGACAGATAATGA-AGCAAGTACAGAGGATAGTGATGTTTTTG
upper sequence: AT5G55060.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G46190.1 (Glycine max), 3'ss of exon 9
gtgatcatcttaatgaataatcttattactgtttggtatataagcactcatgtaaggaaagaaattgtagctgatatgaaatt--gataagatctgtacctc----tgtattagGCAGCAAATCCTGGCTGTATTTTGGAAGATTTTGTGAGATGGCACTCGCCACCAGACTGGACTGAAAATGGTAACATGT-CTGGAGATGACTCTTCACCCG
|| | ||| || | || || || || | | | | | | | | | ||| || || | | | | || |||||| | | | |||||| ||||||||||| ||||| ||||| |||||||| |||||| |||| || || || ||||| || |||| | || || | | ||| | |
gtaaggctctccctggaagggaacttttcttactgacat-tgtgaatgcttcttactatgttgaatgtgcctaatgttcagtctgagttagttctgtatgttatgatattttagGCTGCAAATCCTGGATGTATCTTGGAGGATTTTGTAAGATGGTACTCTCCTCCTGATTGGACAGATAATGA-AGCAAGTACAGAGGATAGTGATGTTTTTG
upper sequence: AT5G55060.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv19s0090g00690.t01 (Vitis vinifera), 3'ss of exon 9
----------------------gtgatcatcttaatgaataatcttattactgtttggtatataagcactcatgtaaggaaagaaattgtagctgatatgaaattga-taagatctgtacctc----tgtattagGCAGCAAATCCTGGCTGTATTTTGGAAGATTTTGTGAGATGGCACTCGCCACCAGACTGGACTGAAAATG------GTAACATGTCTGGAGATGACTCTTCACCCG
| | || || | | ||| | | || | | | | || | | |||| ||| || || || ||| | | ||| | | ||| |||||| ||||||||||| | |||||| |||||||||||||||||||| || || || || |||||||| | || || | || | ||| || |
gtgaagttttactgtgaagaaaatattattcatatttcttgatcctctagatgctgattttttgccttgatatatgaagaaaaaaacatgcgcaaggatcaatctgactgacttctattaattatcatgtcttagGCTGCAAATCCTGGATCTATTTTAGAAGATTTTGTGAGATGGCATTCACCGCCTGATTGGACTGATACTGAGCCTAGTGATGAGTTTAAAGACACCTTTG------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaggaaagaaattgtagctgatatgaaattgataagatctgtacctctgtattagGCAGCAAATCCTGGCTGTATTTTGGAAGATTTTGTGAGATGGCACTCGCCACCAGACTGGACTGAAAATGGTAACATGTCTGGAGATGACTCTTCACCCG
aattgat putative branch site (score: 4)
tacctct putative PPT
atatgaaattgataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatcatcttaatgaataatcttattactgtttggtatataagcactcatgtaaggaaagaaattgtagctgatatgaaattgataagatctgtacctctgtattagGCAGCAAATCCTGGCTGTATTTTGGAAGATTTTGTGAGATGGCACTCGCCACCAGACTGGACTGAAAATGGTAACATGTCTGGAGATGACTCTTCACCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG