Sequence
atgc intronic sequence ATGC exonic sequenceCTCAAAACTATTAGGCGCAGTAGAAGGTTAGTTTTCATTGGCTGTGGTACAAGTTACAATGCTGCCTTGGCTGCAAGACCTTTTGTGGAGGAATTAACTGgtatgccaacttattgtcctgactccttatgtagaaattttagatgtcaacatcagtgacaatatgtattagctacctgtttcttgacccagatacttcttccttgcattatttggacaatag
Basic information
species | Oryza sativa |
transcript | LOC_Os12g03720.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g03720.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G005849_T03 (Zea mays), 5'ss of exon 5
CTCAAAACTATTAGGCGCAGTAGAAGGTTAGTTTTCATTGGCTGTGGTACAAGTTACAATGCTGCCTTGGCTGCAAGACCTTTTGTGGAGGAATTAACTGgtatg-----ccaacttattgtcctgact-------ccttatgtagaaattttagatgtcaacatcagtgacaatatgtattagctacctgtttcttgacccagatacttcttccttgcattatttggacaatag
||||| || ||||||||| |||||||| | || || ||||| ||||| |||||||||||||||||||| |||||||||||||||||||| ||| | ||||||| | ||| | ||| | || | || ||||| || | | || | | | |||| || | || | ||| ||||||| ||||||||| | ||
CTCAAGACAATTAGGCGCTGTAGAAGGGTGGTATTTATTGGTTGTGGAACAAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaatcaattaattactccagctgtattgcctataccaagaaaagtttggaatt--tgtcgaagcaatcagaccttagttaatgatcctttaggtttaac-ctttctccttgctttatttggatgacag
upper sequence: LOC_Os12g03720.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G180155_T01 (Zea mays), 5'ss of exon 1
CTCAAAACTATTAGGCGCAGTAGAAGGTTAGTTTT----CATTGGCTGTGGTACAAGTTACAATGCTGCCTTGGCTGCAAGACC--TTTTGTGGAGGAATTAACTGgtatgccaactta----------ttgtcctgactccttatgtagaaattttagatgt-caacatcagtgacaatatgtattagctacctgtttcttga--cccagatacttcttccttgcattatttggacaatag
| || | |||| | | ||| ||||| ||||| ||||| |||||||||||||||||||| ||||||||||| ||||||||| ||| | ||||||| ||| | | ||| || ||| || | |||||| | || ||| | | | ||| || || || | | |||| | |||| |||| |||| ||||
------ATTAGGCGCTGCAGAAAAGGGTGGGTTTTATTTTATTGGTTGTGGAACAAGTTACAATGCTGCCTTAGCTGCAAGACCCTTTTTGTGGAAGAACTGACTGgtaagcccggtcaattactccagctgtgttgcctctttgtctagaaaaaaaaattggattttgtcaaagcaatcagaacttaattaatgattctttaagttttgcctctttctcctttgctttatctggaggatag
upper sequence: LOC_Os12g03720.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA09G38460.1 (Glycine max), 5'ss of exon 6
CTCAAAACTATTAGGCGCAGTAGAAGGTTAGTTTTCATTGGCTGTGGTACAAGTTACAATGCTGCCTTGGCTGCAAGACCTTTTGTGGAGGAATTAACTGgtatgccaacttattgtcctgactcctta--tgtagaaattttagatgtcaacatcagtgacaatatgtattagctacctgtttcttgacccagatacttcttccttgcattatttggacaatag
|||||||| |||||||| ||||||||| || |||||||||| |||||||||||||| |||||||| ||||| || ||||| | |||| ||| | ||||| || | ||||| | | | | | ||| | | | |||| || |||| | | | | ||| || ||
CTCAAAACAATTAGGCGAAGTAGAAGGATACTTTTCATTGGTTGTGGTACAAGTTATAATGCTGCTTTGGCAGCTAGACCCATCTTGGAAGAACTTTCTGgt----cagtgctgtatcctgtattttaagttttgctgattaaaagtatgcacattcttg-caatgttttattatattttatttattattatag-------------------------------
upper sequence: LOC_Os12g03720.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA18G47860.1 (Glycine max), 5'ss of exon 7
-CTCAAAACTATTAGGCGCAGTAGAAGGTTAGTTTTCATTGGCTGTGGTACAAGTTACAATGCTGCCTTGGCTGCAAGACCTTTTGTGGAGGAATTAACTGgtatgccaacttattgtcctgactccttatgtagaaattttagatgtcaacatcagtgacaatatgtattagctacctgtttcttgacccagatacttcttcct-tgcattatttggacaatag
|||||||| |||||||| ||||||||| || |||||||||| |||||||||||||| |||||||| ||||| || ||||| | |||| ||| | | ||| || | ||||| |||| | |||| || | | || | | | || | || | || || | | || || | | | |||||||
CCTCAAAACAATTAGGCGAAGTAGAAGGATACTTTTCATTGGTTGTGGTACAAGTTATAATGCTGCTTTGGCAGCTAGACCCATATTGGAAGAACTTTCAggt----cagtgctgtatcctg------tatg-acaaatctt---ttttaagtttggctg-attaaaaagta--tgcccattcttacaatgttttattttattttatacattattata-------
upper sequence: LOC_Os12g03720.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv13s0064g00050.t01 (Vitis vinifera), 5'ss of exon 6
CTCAAAACTATTAGGCGCAGTAGAAGGTTAGTTTTCATTGGCTGTGGTACAAGTTACAATGCTGCCTTGGCTGCAAGACCTTTTGTGGAGGAATTAACTGgta--tgccaacttattgtcctga-ctccttatgtagaaattttagatgtcaacatcagtgac-aatatgtattagctacctgtttcttgacccagatacttcttccttgcattatttggacaatag
|| |||||||||||| | || || || | ||||| ||||| ||||| |||||||| |||||||| || ||||||||||| || |||| ||| | | |||| | | | | | ||| | || | || | | ||| | | | | || || | | ||
CTGAAAACTATTAGGAGAAGCAGGAGAATTGTTTTTATTGGTTGTGGCACAAGTTATAATGCTGCTTTAGCTGCAAGACCCATTTTGGAAGAACTTTCAGgtaattactgaatgactgttgggttctgcagatttgacattttcttgtactgatttttccccctgatctggaaaacatag-----------------------------------------------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|8857882|gb|AU095200.1|AU095200EST: AAGTTACAATGCTGCCTTGGCTGCAAGACCTTTTGTGGAGGAATTAACTG GTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
genomic: AAGTTACAATGCTGCCTTGGCTGCAAGACCTTTTGTGGAGGAATTAACTGgtatgccaac ... tggacaatagGTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTCAAAACTATTAGGCGCAGTAGAAGGTTAGTTTTCATTGGCTGTGGTACAAGTTACAATGCTGCCTTGGCTGCAAGACCTTTTGTGGAGGAATTAACTGgtatgccaacttattgtcctgactccttatgtagaaattttagatgtcaacatcagtgacaatatgtattagctacctgtttcttgacccagatacttcttccttgcattatttggacaatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA