Sequence
atgc intronic sequence ATGC exonic sequence...acagacactatattgttactgtattaccagcccaactgctgagatcagacttcaaaccagtacatagtaacacatgtatatgtgtcatttcttattctagGTCGGAAGGTTAAGGAGTCATCAAAGATAGGGCAGTGTCCTCGACCAGAAAAGCCTATCGAGATTTACGAGTTTGAAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g44400.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G882446_T01 (Zea mays), 3'ss of exon 2
--------------------------acagacactat-attgttactgtattaccagcccaactgctgagatcagacttcaaaccagt---------acatag------taa---cacatgtatatgtgtcatttcttattctagGTCGGAAGGTTAAGGAGTCATCAAAGATAGGGCAGTGTCCTCGACCAGAAAAGCCTATCGAGATTTACGAGTTTGAAGG---------------------
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gtgagtttattcacaatttttccattgcagctattattactcctactatatcatggaaaccacaaagaatcgcacaataagatgcagtttgtggaatacatagctctgttaagtttacttgtaaacatg-cgtttcttatcgtagCTTGGAAGGTGAAAGAGGAATCAAAAATAGGACAGTGCAAACGACCAGAAAAGCCTATCGAGATATATGAATTTGAAGGGTACAGCATATCTTGCTTCTT
upper sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G022866_T01 (Zea mays), 3'ss of exon 2
--------------------------------------acagacactatattgttactgtattaccagcccaactgctgagatcagacttc---aaaccagtacatagtaac----acatgtatatgtgtcatttcttattctagGTCGGAAGGTTAAGGAGTCATCAAAGATAGGGCAGTGTCCTCGACCAGAAAAGCCTATCGAGATTTACGAGTTTGAAGG
|| ||||||| || | | | | |||| || || || | ||||| || |||| | || | |||||||| ||| | ||||||| || ||| |||||| ||||| ||||| ||||||||||||||||||||||| || || ||||||||
gtgagtttattcacaattcttccattgcagctattattactcctactatatccttgaaatcacaaagaatcgcacaataagatgcagtttgtggaatacatagctctgtaacgtttacttgtaaacatg-cgtttcttatcgtagCTTGGAAGGTGAAAGAGGAATCAAAAATAGGACAGTGCAAACGACCAGAAAAGCCTATCGAGATATATGAATTTGAAGG
upper sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G804772_T03 (Zea mays), 3'ss of exon 2
--------------------------acagacactat-attgttactgtattaccagcccaactgctgagatcagacttcaaaccagt---------acatag------taa---cacatgtatatgtgtcatttcttattctagGTCGGAAGGTTAAGGAGTCATCAAAGATAGGGCAGTGTCCTCGACCAGAAAAGCCTATCGAGATTTACGAGTTTGAAGG
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gtgagtttattcacaattcttccattgcagctattattactcctactatatcatggaaaccacaaagaatcgcacaataagatgcagtttgtggaatacatagctctgttaagtttacttgtaaacatg-cgtttcttatcgtagCTTGGAAGGTGAAAGAGGAATCAAAAATAGGACAGTGCAAACGACCAGAAAAGCCTATCGAGATATATGAATTTGAAGGMapped 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|58590549|gb|CF988857.1|CF988857EST: GGTTTCTCCTGACGAGGTGGCACCAGATGAATATGCTTTGGATTTCCAAG GTCGGAAGGTTAAGGAGTCATCAAAGATAGGGCAGTGTCCTCGACCAGAAA
genomic: GGTTTCTCCTGACGAGGTGGCACCAGATGAATATGCTTTGGATTTCCAAGgtacaatctt ... cttattctagGTCGGAAGGTTAAGGAGTCATCAAAGATAGGGCAGTGTCCTCGACCAGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagacttcaaaccagtacatagtaacacatgtatatgtgtcatttcttattctagGTCGGAAGGTTAAGGAGTCATCAAAGATAGGGCAGTGTCCTCGACCAGAAAAGCCTATCGAGATTTACGAGTTTGAAGG
tagtaac putative branch site (score: 1)
tcatttcttattct putative PPT
atttcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acagacactatattgttactgtattaccagcccaactgctgagatcagacttcaaaccagtacatagtaacacatgtatatgtgtcatttcttattctagGTCGGAAGGTTAAGGAGTCATCAAAGATAGGGCAGTGTCCTCGACCAGAAAAGCCTATCGAGATTTACGAGTTTGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
acagaca
- - - - - - -tgttact
- - - - - - - - - - - - taccagc
- - - - - - - - - - - - - - - - - actgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaaccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtat