Sequence
atgc intronic sequence ATGC exonic sequencegtaaatataatcaaacttcttttggttatatactgttcttgatcttaccttaacagtgttttatttgaccagACAATTGCTGTGATTCAAGCTGGACATGGTCTGTTACAGCTAGGTTCTTGCAAGATT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53900.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G34980.1 (Glycine max), 3'ss of exon 5
-----------------------------------gtaaatataatcaaacttcttttggttatatactg---ttcttgatcttaccttaacagtgttttatt---tgaccagACAATTGCTGTGATTCAAGCTGGACATGGTCTGTTACAGCTAGGTTCTTGCAAGATT
| ||| || |||| | || | | || | | | | ||| |||| || ||||||||| || ||||| |||||||||||||||||||| | || || |||||||||||||||
gtcagtaacagaatcgttgttggttttgtttggcttttgttattattgctcttcacaagatttctttttagatttttcaacccaaatttattttctttttgttccatgaccagACCATAGCTGTTATTCAAGCTGGACATGGTCTTCTCCAACTTGGTTCTTGCAAGATT
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G27400.1 (Glycine max), 3'ss of exon 5
-------------------------------------------gtaaatataatcaaacttcttttggttatatactgttc---ttgatcttaccttaacagtgttt--tatttgaccagACAATTGCTGTGATTCAAGCTGGACATGGTCTGTTACAGCTAGGTTCTTGCAAGATT
| || | | | || | |||| | | | || || | ||| ||| | ||| | | ||||||||| ||||||||||||||||| ||||| || | || || |||||||||||||||
gtgagggacaaaatgaattaacagcatgctattattggtctcagaaagtttttttaatgtactttaaagtttcaatcatttcattttcttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G36190.1 (Glycine max), 3'ss of exon 5
-------------------------------------------gtaaatataatcaaacttcttttggttatatactgttc---ttgatcttaccttaacagtgttt--tatttgaccagACAATTGCTGTGATTCAAGCTGGACATGGTCTGTTACAGCTAGGTTCTTGCAAGATT
| || | ||| | |||| | | | || || | ||| ||| | ||| | | ||||||||| ||||||||||||||||| ||||| || | || || |||||||||||||||
gttagggccaaaatgaattaacagcatgctattattgatctcagaaagcttttccaatgtactttaaagtttcaatcatttcatttacttttattttatttgcatttattccattgccagACAATCGCTGTGATTCAAGCTGGGCATGGCCTTCTGCAACTTGGTTCTTGCAAGATT
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G35490.2 (Glycine max), 3'ss of exon 4
---------------------------------------------gtaaatataatcaaacttcttttggttatatactgttcttgatcttaccttaacagtgttttatt-tgaccagACAATTGCTGTGATTCAAGCTGGACATGGTCTGTTACAGCTAGGTTCTTGCAAGATT
| | || | | ||||||| || | | | || ||| || |||| || ||||||||| || ||||| ||||||||||||||||| || | || || |||||||||||||||
gtcagtaacagaatcattgttagctttgtttggcttttgttattattggtcttcatgagatttctttttaagatttttcatccc-aattttat-ttgcttttgttccatgatgaccagACCATAGCTGTTATTCAAGCTGGACATGGCCTTCTCCAACTTGGTTCTTGCAAGATTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|124881202|gb|EH960104.1|EH960104EST: CTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAG ACAATTGCTGTGATTCAAGCTGGACAT
genomic: CTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAGgtaaatataa ... atttgaccagACAATTGCTGTGATTCAAGCTGGACAT
EST:
gi|124861062|gb|EH945499.1|EH945499EST: CCGACCAATTCGAATCAGGCATTCAG ACAATTGCTGTGATTCAAGCTGGACATGGTCTGTTACAGCTAGGTTCTTGC
genomic: CCGACCAATTCGAATCAGGCATTCAGgtaaatataa ... atttgaccagACAATTGCTGTGATTCAAGCTGGACATGGTCTGTTACAGCTAGGTTCTTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttggttatatactgttcttgatcttaccttaacagtgttttatttgaccagACAATTGCTGTGATTCAAGCTGGACATGGTCTGTTACAGCTAGGTTCTTGCAAGATT
ccttaac putative branch site (score: 3)
ttttattt putative PPT
tgttttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatataatcaaacttcttttggttatatactgttcttgatcttaccttaacagtgttttatttgaccagACAATTGCTGTGATTCAAGCTGGACATGGTCTGTTACAGCTAGGTTCTTGCAAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA