Sequence
atgc intronic sequence ATGC exonic sequenceGCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAGgtattatttgtgttgacttttgcaatatggatacaacctttgtactaaatttgtccagaaacttgatattcaaatacggtaatatttgtggatggaatgtgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g03400.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g03400.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G089860_T02 (Zea mays), 5'ss of exon 4
GCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAGgtattatttgtgttgacttttgcaatatggatacaacctttgtactaa--atttgtccagaaacttgatattcaaatacggtaatatttgtggatggaatgtgcag
||| |||||||||||| |||||||||||| |||||||| |||||||| ||||||||||||||| | | | | ||| ||| | ||||| | | | | | ||| | | | | | | || | | | || || | | |||| || ||
GCTATAAAGGATGGGGTTGATGCCGTGATAGCTGTTGGAGGTGATGGTACACTTCATGAGgtactttgtttattg-----cacaaccatgctacaaacagttttccagcgattgatactggtataacagttacagagttgatgatgttatt---ttgaatatgtag
upper sequence: LOC_Os03g03400.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G382537_T01 (Zea mays), 5'ss of exon 5
GCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAGgtattatttgtgttgacttttgcaatatggatacaacctttgtactaa--atttgtccagaaacttgatattcaaatacggtaatat--ttgtggatg-------gaatgtgcag--------------------------------------------------------------------------------------
||| ||||||||||||||||||| ||||| |||||||| |||||||| || ||||||||||| | | | || | || | || ||| ||||| | ||| || ||| | | |||||| |||| || ||| ||| ||||| |||| || ||
GCTATAAAGGATGGGGCTGATGCTGTGATCGCTGTTGGAGGTGATGGTACGCTTCATGAGgtgctttctttgcacatttgtacattatttgctcaaccatgctacaaacagtttaatttttcagt-gatattgtgataccgttatagagttgaggatgctattttgaatatgtaggtgcctatggtttcttttggaaaggaacattgtttcttctatacactggggtttgtttagtagtgaagtaccttgtcctctgacag
upper sequence: LOC_Os03g03400.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G39010.1 (Glycine max), 5'ss of exon 4
GCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAGgtattatttgtgttg--acttttgcaatatggatacaacctttgtactaaatttgtccagaaacttgatattcaaatacggtaatatttgtggatgga-atgtgcag-
||| ||| ||| |||||||||||||| ||||||||||| ||||||||||| ||||||||||| ||| || | |||| | | | || || || ||||| | || | || | | | ||| | | |||| ||
GCTATAAGGGAGGGGGCTGATGCCGTCATTGCTGTTGGAGGTGATGGAACTCTTCATGAGgtgaagactgtttttttatttttttattgttgagac--------taaagaattttccaagggaattcttgagtagcatccaccttatcagaaagggttcatgttcaac
upper sequence: LOC_Os03g03400.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA18G47330.1 (Glycine max), 5'ss of exon 4
-GCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAGgtattatttgtgttgacttttgcaatatggatacaacctttgtactaaatttgtccagaaacttgat--attcaaatacggtaatatttgtggatggaatgtgcag
||| ||| ||| ||||||||||| || ||||||||||| || |||||||| ||||||||||| | || | ||| ||| | | | || |||| | | | | | | ||||| ||| | | | |||| | || || |
GGCTATAAGGGAGGGGGCTGATGCTGTCATTGCTGTTGGAGGAGATGGAACTCTTCATGAggtgaaaactgc-----ccttttcaaaaaaaaaataattattgttgggagtgt-tgatgttatttgatggatttattgctacttaaatttctacataaaaaatttc-
upper sequence: LOC_Os03g03400.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT2G46090.1 (Arabidopsis thaliana), 5'ss of exon 4
GCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAGgtattatttgtgttgacttttgcaatatggatacaacctttgtactaaatttgtccagaaacttgatattcaaatacggtaatatttgtggatggaatgtgcag
||| ||| |||||| || ||||| || ||||| ||||| |||||||||||||||||||||||| | ||| | ||||| | | || ||| | | || | | || | |||| | | ||| | | |
GCTATAAGGGATGGTGCAGATGCTGTCATTGCGGTTGGAGGTGATGGAACACTTCATGAGgtaggaattgcc---atttttg----gttgctagaac-tgcgctctggagat-tcttagctccactcattctgtcctttttttttttatctacag---------
upper sequence: LOC_Os03g03400.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv15s0046g01770.t01 (Vitis vinifera), 5'ss of exon 4
GCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAGgtattatttgtgttgacttttgcaatatggatacaacctttgta-ctaaatttgtccagaaacttgatattcaaa----tacggtaatatttgtggatggaatgtgcag
|| || ||| || ||||||||||||||||| ||||| || |||||||| ||||||||||| ||||| | ||| ||| | | || |||| ||| | | | ||| | | | | || || || | || | |||||
GCCATACGGGAGGGTGCTGATGCCGTGATTGCAGTTGGAGGGGATGGAACTCTTCATGAGgtgc-atttgcttctcttttagcatgaaagctagtttatttgcgtctataacaatttacaaaatcttttccccaccttttagggcaac-tatgctggtggaa-------Mapped 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|58682220|gb|CK070907.1|CK070907EST: GGGGCTGATG-CGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAG GTCGTCGATGG-TTCTTCTGTAAGGGAAGTCCTGTCCATGCTCTTGATCAA
genomic: GGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAGgtattatttg ... gaatgtgcagGTCGTCAATGGCTTCTTCTGTAAGGGAAGTCCTGTCCATGCTCTTGATCAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCTGTAAAGGATGGGGCTGATGCCGTGATTGCTGTTGGTGGTGATGGAACACTTCATGAGgtattatttgtgttgacttttgcaatatggatacaacctttgtactaaatttgtccagaaacttgatattcaaatacggtaatatttgtggatggaatgtgcag
- - - - - - - GCTGAT
- - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - GATGGA