Sequence
atgc intronic sequence ATGC exonic sequencegtatataatgcgatgttgcaatgatgcttcttccttctttcatggcgggctcggtaggacgcgatctgattggcatttttgcattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g21160.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G003424_T01 (Zea mays), 3'ss of exon 2
gtatataatgcgatgttgcaatgatgcttcttccttctttcatggcgggctcggtaggacgcgatctgattggcatttttg--cattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG
|||| | | | |||| || | || | ||||| | || |||| || | | || ||||| ||| ||| || |||||| || ||| |||||||||||||| || || ||||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| ||| ||
gtatgcatgcacacacggtaatg-tgatgctccaatcttt-------gcttccgtagaaccccgtttggttggctgacttgaccatcgcgcttcttgttg--gcaatgcggtgcagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTACCCAGAGACGGTGAAGCTCATCCTG
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G819035_T01 (Zea mays), 3'ss of exon 3
gtatataatgcgatgttgcaatgatgcttcttccttctttcatggcgggctcggtaggacgcgatctgattggcatttttg--cattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG
|||| | | | |||| || | || | ||||| ||| || |||| | | | || ||| ||| | | || ||||| |||| || | || ||||||||||| || || ||||||||||||||||| |||||||||||||||||||||||||||||||||||||| || || ||||| |||||||| ||| ||
gtatgcatgcacacacggtaatg-tgatgctccaatcttt----gcg---tccgtagaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatgc-----ggtgtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G086614_T01 (Zea mays), 3'ss of exon 2
gtatataatgcg-----atgttgcaatgatgcttcttccttctttcatggcgggctcggtaggacgcgatctgattggcatttttgcattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG
|||| |||| | | |||| || || | || | || | || | || || | | || |||| || | | || |||||||||| ||| ||| ||||||||||| || || |||||||||||||| || |||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| ||| ||
gtatgctatgcatgcacacatgttaatg-tgattgatgctgcaatctttgcttcggtagaagaaccccgtttggttgg---ttgaccctcgcgcttcttggcaatgcggcgc-----agCATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCAGAGACGGTGAAGCTCATCCTG
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G35980.1 (Glycine max), 3'ss of exon 3
gtatataatgcgatgttgcaatgatgcttcttccttctttcatggcgggctcggtaggacgcgatctgattggcatttttgcattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG
|| || ||| | | | | | | |||| | | | | | | || || | | ||| || | | || ||||| || || || ||||| |||||| | ||||| |||||||||||||| ||||| || || || ||||| ||||| || ||||| |||||||| || |
gttattattgcttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttggtcagcggcagaaatattaacttga--gtttttaattctgt----tgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G01340.1 (Glycine max), 3'ss of exon 3
gtatataatgcgatgttgcaatgatgcttcttccttctttcatggcgggctcggtaggacgcgatctgattggcatttttgcattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG
| ||| | | ||| || | | | | | ||| | | || | || || | || ||| || | | || ||||| || || || || || |||||| | ||||| |||||||||||||| ||||| || || || ||||| ||||| || ||||| |||||||| || |
--------gttattattgtttaggtttaactttgttaactggggtcagtgtgcatagttggtcaa-tggcagaaatattaac-ttatagtttttatttctgt----tgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G01350.1 (Glycine max), 3'ss of exon 2
gtatataatgcgatgttgcaatgatgcttcttccttctttcatggcgggctcggtaggacgcgatctgattg--gcatttttgcattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG
| | || | | | | ||| || | | || | || | ||| | | | | || || ||| || | | || ||||| || || || || || |||||| | ||||| |||||||||||||| ||||| || || || ||||| ||||| || ||||| |||||||| || |
-----------gttattattgtt-taggtttaactttgttaactggggtcagtgtgcatagttggtcgatggcagaaatattaacttatagtttttatttctgt----tgttgaagCATATATGGTCCTGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G63450.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatataatgcgatgttgcaatgatgcttcttccttctttcatggcgggctcggtaggacgcgatctgattggcatttttgcattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG
| || | | ||| | || | ||| || ||| || | ||| || | | ||||| | | ||||| || || |||||| | || || |||||||||||| | ||||| |||||||| |||||| | ||||| ||||| |||||| || ||
-----------------------------------------gtattactcttgtttggaacccat-tcattcttcttgttggat-gttgtctacttaaagcaatggtggtgcagTACGTTTGGGCCAGTTCAGGACGTGAGGATACCTTACCAGCAGAAGAGGATGTTTGGGTTCGTGACCTTCATGTACCCAGAGACTGTGAAGAGCATTCTG
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
gtatataatgcgatgttgcaatgatgcttcttccttctttcatggcgggct-cggtaggacgcgatct---gattggcatttttgcattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG
|| | | | || || || ||||| || | | | | || | | | || || | |||| ||| | || |||||| | | | | || ||||| | ||| || || || || ||| | ||||| || ||||||||| | ||||||||||| || ||||||||||| || ||||| |||||||| || |||
gttttgaccacaattttcatgaattgtttcttggttttgtgcaattgaattgtgggaagttgagagctttcggttgg--tttctaaatcgctgtttt--gttttgt----tgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
gtatataatgcgatgttgcaatgatgcttcttccttctttcatggcgggctcggtaggacgcgatctgattggcatttttgcattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG
|||| || | | || || || || |||| ||| | || | || | || | | ||| ||| ||| ||| || || || | ||||| || || || ||| | || || |||||||||||| | |||||||| |||||||| ||||| ||||| ||||| |||||||| || ||
----gtaat----tgctacg-tgttggttggaaatttcttcaatttggggttcgtgttgtgaaatttagttaacctagttggcttg-tgtgctt--------------ttgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTAMapped 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|163928946|gb|EG711958.1|EG711958EST: TTCCCGGCCGACAGCACGTTCCGCGAGGAGGACGTCTCCAACTACTTCAG CATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
genomic: TTCCCGGCCGACAGCACGTTCCGCGAGGAGGACGTCTCCAACTACTTCAGgtatataatg ... cgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgcgatctgattggcatttttgcattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG
atctgat putative branch site (score: 4)
attttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatataatgcgatgttgcaatgatgcttcttccttctttcatggcgggctcggtaggacgcgatctgattggcatttttgcattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT