Sequence
atgc intronic sequence ATGC exonic sequencegtaattctaaggacagtgtcctggcagatttgattctagaaacattttggcattttgccaagggtgtttatatgttgctccatttaattgttccagAGATAGCAAACTGACAAGATTGCTAAGAGACTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCCACAATATCACCTTCAGTATATTGTTTGGAAGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g02670.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g02670.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 5
gtaattctaaggacagtgtcctggcagatttgattctagaaacattttggcattttgccaagggtgtttatatgttgctccatttaattgttccagAGATAGCAAACTGACAAGATTGCTAAGAGACTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCCACAATATCACCTTCAGTATATTGTTTGGAAGAG
|||| ||||| | | | || ||| ||||||| ||| |||| ||| | | | |||||| ||| || || ||||| ||||||||| ||||||||||| ||||| || || ||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
gtaaccctaagaatggc-ccttgacagctttgattttagtaacacgttg------ctcaatgatggtttatgtgt------atctatttgtttcagAGATAGTAAACTGACAAGGTTGCTGAGGGATTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCTACAATATCACCTTCAGTATATTGTTTGGAAGAG
upper sequence: LOC_Os05g02670.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA15G04830.1 (Glycine max), 3'ss of exon 5
gtaattctaaggacag--tgtcctggcagattt-gattctagaaacattttggcattttgccaagggtgtttatatgttgctccatttaattgtt---ccagAGATAGCAAACTGACAAGATTGCTAAGAGACTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCCACAATATCACCTTCAGTATATTGTTTGGAAGAG
||| ||| || | || || || | | ||| | |||| ||||| | | | || ||| | | || | ||| || ||||||||||||| | || |||||| | || || || ||||| || ||||| || || |||||||||||||||||||| ||||| | | ||| |||||||
gtatgagtaactgcaacttttcttgtcaattctcaatttcattttttttttattattttctgagtgattttattattaagatatatcttattattatatcagAGATAGCAAATTAACCAGATTGTTGAGGGATTCTTTGGGTGGTAAAACCAAAACGTGCATTATTGCCACAATATCCCCTTCCATTCACTGTCTGGAAGAA
upper sequence: LOC_Os05g02670.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv06s0004g03810.t01 (Vitis vinifera), 3'ss of exon 6
-----------gtaatt--ctaaggacagtgtc-ctggcagatttgattctagaaacattttggcattttgccaagggtgtttatatgttgctccatttaattgttccagAGATAGCAAACTGACAAGATTGCTAAGAGACTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCCACAATATCACCTTCAGTATATTGTTTGGAAGAG
||||| | || | | | | ||||| || | || | | || | | || ||| ||| | | | | || | | ||| ||||||||| | ||||| || | || || || ||||||||||||||||| || ||||| |||||||||||||| || || | | || |||||||||
gtatgaactgcataattagttcagtaaattattattggcatatgaggtttgattttgaacttagaaattgaggtgaggtaattaaaaa--gattgcctgaaatat--cagGGATAGCAAATTAACAAGGTTATTGAGGGATTCCTTGGGAGGGAAAACAAAAACATGCATAATTGCCACAATATCGCCCTCCATTCACTGCTTGGAAGAG
upper sequence: LOC_Os05g02670.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S13_177V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------gtaattctaaggacagtgtcctggcagatttgattctag----aaacattttggcattttgccaagggtgtttatatgttgctccatttaatt-------gttccagAGATAGCAAACTGACAAGATTGCTAAGAGACTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCCACAATATCACCTTCAGTATATTGTTTGGAAGAG
| | | |||| |||| | ||| | | || ||| | | ||| | | || | | || | | | | |||||||||||| |||||||||||| |||| || || |||||||| || |||||||| |||||||||||||| | || || || || |||| | |||||
gtaatttgtcctctgttgtgactatttgctggagtgacaaattccttcccagttttgtgttgattataattgtttctatttctattttcaactgtatgcctaatgtttctcttgacttcgtatggatacagAGATAGCAAGCTGACAAGATTGTTAAGGGATTCTTTGGGAGGAAAGACAAAGACCTGCATTATTGCCACCGTTTCGCCCTCCGTTCATTGCCTTGAAGAA
upper sequence: LOC_Os05g02670.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S158_7V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaattctaaggacagtgtcctggcagatttgattctagaaacattttggcattttgccaagggtgtttatatgttgctccatttaattgttccagAGATAGCAAACTGACAAGATTGCTAAGAGACTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCCACAATATCACCTTCAGTATATTGTTTGGAAGAG
|| | ||| | | ||| | || | | | || | | | | || || | | | | ||| ||||| || |||||||||||| ||||||||| |||| |||| || |||||||||| ||||||||| ||||| || ||||| |||| || || || | ||| |||| ||
gtgaatcttatgtcagcggccatata-acctctctcgtccagtacagagttccctctcctagagcttaattctcttgtc---gttaatgtttacagAGATAGCAAGCTGACAAGACTGCTCCGAGATTCTTTGGGAGGGAGAACAAAGACATGCATCATCGCCACTGTATCTCCATCTGTTCAATGTCTGGACGAAMapped 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|58664623|gb|CK053309.1|CK053309EST: GGTCGAGTCATCAATGCTCTTGTTGAACACTCTGGACATGTCCCATACAG AGATAGCAAACTGACAAGATTGCTAAGAGACTCATTGGGAGGGAAAACAAA
genomic: GGTCGAGTCATCAATGCTCTTGTTGAACACTCTGGACATGTCCCATACAGgtaattctaa ... attgttccagAGATAGCAAACTGACAAGATTGCTAAGAGACTCATTGGGAGGGAAAACAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acattttggcattttgccaagggtgtttatatgttgctccatttaattgttccagAGATAGCAAACTGACAAGATTGCTAAGAGACTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCCACAATATCACCTTCAGTATATTGTTTGGAAGAG
atttaat putative branch site (score: 4)
ttgttcc CT-rich tract
atttaattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattctaaggacagtgtcctggcagatttgattctagaaacattttggcattttgccaagggtgtttatatgttgctccatttaattgttccagAGATAGCAAACTGACAAGATTGCTAAGAGACTCATTGGGAGGGAAAACAAAGACTTGCATTATTGCCACAATATCACCTTCAGTATATTGTTTGGAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA