Sequence
atgc intronic sequence ATGC exonic sequence...gtaaccatatatgttcccttggcattattagtcttgccaaatctcatttgtacaagttttccgctcacatttcttatttgttaatcttttatatatgcagATCAGCGTCTCAATGATGTTGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTCCATAGGTCTTACAGCACTGAAGCAGATATGTGGAGCATCGGTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G24430.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G24430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os10g36710.1 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------------------gtaaccatatatgttccct-------tggcattattagtctt----gccaaat--ctcatttgtacaagttttccg------ctcacatttcttatttgttaatcttttatatatgcagATCAGCGTCTCAATGATGTTGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTCCATAGGTCTTACAGCACTGAAGCAGATATGTGGAGCATCGGTGT
| || || | ||| || | || | | || |||||| | | ||||| || | | || |||| | ||| || ||| || | | | ||||| | | | |||||| |||| || ||||||||||||||||| || ||||| || |||||||| || ||||| |||||||| |||||||| || |||||
gtatttccccccaaaagaattatgcccttccaaagaacttgtgtttcatcttatgttttttttttactctattatgaatttgtcctgacatggtgaaaatactgttttttgaaaccaaatagtgaaaatactcaagtgttttgatgacacacatatttatgattggtcaatgccttcttt-tacagATGAAAGATTAAATGATATTGTTGGTAGTGCATACTATGTTGCTCCAGAAGTCCTACATAGGTCATATAGCACGGAAGCAGACATGTGGAGTATTGGTGT
upper sequence: AT5G24430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G031893_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------gtaaccatatatgt--tcccttggcatt--attagtcttgcca-aatctcatttgtacaagttttccgctcacatttcttatttgttaatcttttatatatgcagATCAGCGTCTCAATGATGTTGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTCCATAGGTCTTACAGCACTGAAGCAGATATGTGGAGCATCGGTGT
|| || | | ||| ||| ||| || | | || | | || | | || | ||| | | | | | | || | | ||||| | | || ||||| |||| |||||||||||||||||||| || ||||| | |||||||| || ||||| |||||||| ||||||||||| |||||
gtattacatacctccgcacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgacataaaatgaaacatgatatgaccttcctccaaaaaatgttctaacgcctgatgctcctgatgccttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGCATTGGTGT
upper sequence: AT5G24430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G100560_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------gtaaccatatatgt--tcccttggcatt--attagtcttgcca-aatctcatttgtacaagttttccgctcacatttcttatttgttaatcttttatatatgcagATCAGCGTCTCAATGATGTTGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTCCATAGGTCTTACAGCACTGAAGCAGATATGTGGAGCATCGGTGT
|| || | | ||| ||| ||| || | | || | | || | | || | ||| | | | | | | | || | | ||||| | | || ||||| |||| |||||||||||||||||||| || ||||| | |||||||| || ||||| |||||||| |||||||| || |||||
gtattacatacctccacacaagggccatccaattgtaaagttctgttttacaaatatgttagaagtccattgccataaaatgaaacatgatatgaccttcctccaaaaaatgttctaatgcctgatgctcctgatgctttttccccctttacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTATGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGAATTGGTGT
upper sequence: AT5G24430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G138245_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------gtaaccatat--atgttcccttggcatt--attagtcttgccaaatctcatttgtacaagttttccgctcacatttcttatttgttaatcttttatatatgcagATCAGCGTCTCAATGATGTTGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTCCATAGGTCTTACAGCACTGAAGCAGATATGTGGAGCATCGGTGT
|| || | ||| ||| ||| | | | || | | || ||| | | | | || | | ||||| | | || ||||| |||| |||||||||||||| ||||| || ||||| | |||||||| || ||||| |||||||| |||||||| || |||||
gtattacatacctccacacaaggatcatccattcctaatggagttctattttacaaatatgttagaagtccattgacataaaacgaaacatgatatgagcttcctctaaaagatgttttaaagcctgatgctcctgatgcctcctccccctcacagATGAAAGGCTTAATGACATTGTTGGAAGTGCATACTACGTTGCTCCAGAAGTCTTGCATAGGTCATATAGCACAGAAGCAGACATGTGGAGTATTGGTGT
upper sequence: AT5G24430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G13920.1 (Glycine max), 3'ss of exon 5
--gtaaccatatatgttcccttggcattattagtcttgcca-----aatctcatttgtacaagttttccgctcacatttcttatttgttaatcttttatatatgcagATCAGCGTCTCAATGATGTTGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTCCATAGGTCTTACAGCACTGAAGCAGATATGTGGAGCATCGGTGT
|| ||| || |||| | ||||| | || || | | |||| | || || ||| | || | | || | |||||||||| || ||||||||| |||| || ||||| |||||||||||||||||||| |||||||| ||||| || ||||| ||| | ||||| || || ||
cagtgtttgc-tataaattgttatcatttattctcttgtaatcggtgatatcctcttgttggttttttcactaccagctctgacttctaa------taaacatgcagATCAACGCCTCAATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGCTCCATAGATCTTATAGTGTTGAAGGAGACTTATGGAGTATTGGGGT
upper sequence: AT5G24430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G40920.1 (Glycine max), 3'ss of exon 5
gtaaccat-atatgttcccttggcattattagtcttgcca-----aatctcatttgtacaagttttccgctcacatttcttatttgttaatcttttatatatgcagATCAGCGTCTCAATGATGTTGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTCCATAGGTCTTACAGCACTGAAGCAGATATGTGGAGCATCGGTGT
| | | || || |||| | |||||| | || || | | || |||| || || || | || || || | |||||||||| || |||||||| |||| || ||||| ||||| |||||||||||||| |||||||| |||||||| ||||| ||| | ||||| || || ||
ccagttttgaaataaatagttatcatttattgtcttgtaatcagtgatatcctcttattaattttttgactaccagcactgactt------ctactaaacatgcagATCAACGCCTCAATGACATTGTTGGCAGTGCCTACTACGTTGCACCTGAAGTGCTCCATAGATCTTACAGTGTTGAAGGAGACTTATGGAGTATTGGGGT
upper sequence: AT5G24430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv16s0098g01140.t01 (Vitis vinifera), 3'ss of exon 5
gtaaccatatatgttcccttggca-ttattagtcttgccaaatctcatttgtacaagttttccgctcacattt---cttatttgttaa-tcttttatatatgcagATCAGCGTCTCAATGATGTTGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTCCATAGGTCTTACAGCACTGAAGCAGATATGTGGAGCATCGGTGT
| | ||| | | || | | ||| | |||| | | | || ||| || | ||| || || | |||||||| || |||||| |||||||||||| |||| ||||||||||||||||||||||| ||||||||||| || || |||| |||||| ||| | |||||||| || ||
-----tgtttcaactccttagacaatcacctctctctctctctctcgtgtttgcactgattcatcttaagtttgaatgtaacagtcagctcttttatgcttgtagATCAACGTCTCAATGATATTGTTGGAAGTGCATACTATGTTGCACCCGAAGTACTCCACAGATCCTACAATCTTGAAGCTGATGTTTGGAGCATTGGCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgtacaagttttccgctcacatttcttatttgttaatcttttatatatgcagATCAGCGTCTCAATGATGTTGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTCCATAGGTCTTACAGCACTGAAGCAGATATGTGGAGCATCGGTGT
tgttaat putative branch site (score: 3)
tcttttat CT-rich tract
acatttcttatttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaccatatatgttcccttggcattattagtcttgccaaatctcatttgtacaagttttccgctcacatttcttatttgttaatcttttatatatgcagATCAGCGTCTCAATGATGTTGTAGGAAGTGCATACTATGTTGCACCTGAAGTACTCCATAGGTCTTACAGCACTGAAGCAGATATGTGGAGCATCGGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- aaccata
- - - - - - - - - - - - - - - - - - ccaaatc