Sequence
atgc intronic sequence ATGC exonic sequencegtaaactcctcttttttttttggtatatgcaaatgtaatgcttatttgagatatccatatttaacctgctctaatttttgttttcaccagATGGCTGAATATAGGATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g28180.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 10
-------gtaaactcctcttttttttttggtat--atgcaaatgtaatgcttatttgagatatccatatttaacctgctctaatttttgttttcaccagATGGCTGAATATAGGATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTG
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gtaaactgtcagctggataacttttttagtttttaattcagaagtacttcttatttgatatcttgttactttat---ccctaatatgctatttca---gATGGCAGAATATAGGATTTCAATCTACGGAAGGAAACAGAGTGAATGGGACCAACTTGCAAGTTGGATAGTGAACAATGAATTGCACAGTGGAAATGTTG
upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 10
---------------gtaaactcctcttttttttttggtatatgcaaatg-taatgcttatttgagatatccatatttaacctgctctaatttttgttttcaccagATGGCTGAATATAGGATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTG
||| | | ||| || || | | | | ||| | || | || | |||| | | | | | || | | || | | ||||| |||||||||||||||| || ||||| ||||| |||||||||||||| |||||| | || || || ||||||||||| ||||| |||| |||||| |||||||
tttgacttgttgactataatttaccatttcttgactgttgtttatatatgcttatccccatct-agatgttaacttat----ttctgtgacttatttattcac-agATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGTGAGAATGTTG
upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 11
---------------gtaaactcctcttttttttttggtatatgcaaatg-taatgcttatttgagatatccatatttaacctgctctaatttttgttttcaccagATGGCTGAATATAGGATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTG
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ttggacttgttgacaataatttaccatttcttgactgtagtttatatatgctcatccccatct-agatgttaacttat----ttctgtgccttatttattcac-agATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 10
gtaaactcctcttttttttttggtatatgcaaatgtaatgcttatttgagatatccatatttaacctgctct---aatttttgttttcac-----------cagATGGCTGAATATAGGATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTG
| || || | | | || ||| || || | | | |||| || | |||||| || | | |||| || | | |||||||||||||| ||||| ||||| ||||| || ||||||||||| |||||| | ||||| || ||||||||||| ||||| |||| |||||| |||||||
agggaatcttcatctgcatgtg-tatgagcccatctgtttttgattt---atttgtttatttattatggtttgtaaattcctgatgctaaatgctatgctacagATGGCTGAATACAGGATATCAATATATGGCAGAAAGCAAAGTGAGTGGGACCAACTTGCCAGTTGGATAGTGAATAATGATTTGTACAGTGAGAATGTTG
upper sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S307_76V6.1 (Physcomitrella patens), 3'ss of exon 10
-------------------------------------------------------------------------------------gtaaactcctc--------ttttttttttggtatatgcaaatgtaatgcttatttgagatatccatatttaacctgctctaatttttg---ttttcac---cagATGGCTGAATATAGGATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTG
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gtaaacatctacaacttcttttcaattaaatttttttattagatgtttttgtactccattttgaaataccacttctgcccaattcacaaccccaccacacaaggttttgagtgagcaacacacatgggttttgagtttttgaggggcatgaagtccattgaatcccatcaacagcatattcactttcagATGGCAGAGTATAGAATTTCTATCTATGGGAGGAAGGAAAGTGAATGGGACCAGTTAGCCAGTTGGATTGTCACTAACAAACTTCAAAGTGAGAATGTGAMapped 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|58687285|gb|CK075972.1|CK075972EST: CCGAGCTAACAAAGCAAGTTTTCTCCGACCTTACAGCAAGTAAATACCAG ATGGCTGAATATAGGATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGAC
genomic: CCGAGCTAACAAAGCAAGTTTTCTCCGACCTTACAGCAAGTAAATACCAGgtaaactcct ... ttttcaccagATGGCTGAATATAGGATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGAC
EST:
gi|58610210|gb|CK038109.1|CK038109EST: CCGAGCTAACAAAGCAAGTTTTCTCCGACCTTACAGCAAGTAAATACCAG ATGGCTGAATATAGGATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGAC
genomic: CCGAGCTAACAAAGCAAGTTTTCTCCGACCTTACAGCAAGTAAATACCAGgtaaactcct ... ttttcaccagATGGCTGAATATAGGATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatgcttatttgagatatccatatttaacctgctctaatttttgttttcaccagATGGCTGAATATAGGATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTG
ctctaat putative branch site (score: 3)
tttttgttttcacc CT-rich tract
tctaatttttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaactcctcttttttttttggtatatgcaaatgtaatgcttatttgagatatccatatttaacctgctctaatttttgttttcaccagATGGCTGAATATAGGATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA