Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatcactcttttgtgacttgaaactattgtcttgtgctactgcatcagcctaagtggcatatgctttgcatattttggcatgacttgataagttactccgcaaccttgtttggtctgatgggctgccctttacaataccacagATAGGCTATCTGGTGTCATGGATGATCGTGGGAAGTTCATATACATATCTACTGAGGAGATGAAGGCTGTCGCAGATTACATCAGGAAACAAGGGAGGGT
Basic information
species | Oryza sativa |
transcript | LOC_Os07g01320.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g01320.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G179429_T03 (Zea mays), 3'ss of exon 6
-----------gtatgtatcactcttttgtgacttga-aactattgtcttgt--gcta-ctgcatcagcctaagtggcatatgctttgcatattttggcatgacttgat---aagttactccgcaaccttgtttggtct-gatgggctgcccttt----acaataccacagATAGGCTATCTGGTGTCATGGATGATCGTGGGAAGTTCATATACATATCTACTGAGGAGATGAAGGCTGTCGCAGATTACATCAGGAAACAAGGGAGGGT----
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gtgacttttgtttagatttggcttcccttcaattggttaaccgtgaataagcccgctaacctgatgattcctagctacatatcctggcggcagtgagaaactgtctgccgccaaagccctcaacagttttttttagttttgctaagcctttttttttgcatgtaacaacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGAAGAGATGAAGGCAGTTGCAGAGTACATTAGGAAGCAAGGGAGAGTGAGC
upper sequence: LOC_Os07g01320.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G179429_T01 (Zea mays), 3'ss of exon 6
gtatgtatcactcttttgtgacttgaaactattgtcttgtgctactgc--atcagcctaagtggcatatgctt------tgcatattttggca------------tgact--tgataagttactccgcaaccttgtttggtct-gatgggctgcccttt----acaataccacagATAGGCTATCTGGTGTCATGGATGATCGTGGGAAGTTCATATACATATCTACTGAGGAGATGAAGGCTGTCGCAGATTACATCAGGAAACAAGGGAGGGT
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gtatgtgacttttgtttagatttggcttcccttcaattggttaaccgtgaataagcccgctaacctgatgattcctagctacatatcctggcggcagtgagaaactgtctgccgccaaagccctcaacagttttttttagttttgctaagcctttttttttgcatgtaacaacagATAGGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGAAGAGATGAAGGCAGTTGCAGAGTACATTAGGAAGCAAGGGAGAGT
upper sequence: LOC_Os07g01320.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ23839 (Selaginella moellendorffii), 3'ss of exon 7
gtatgtatcactcttttgtgacttgaaactattgtcttgtgctactgcatcagcctaagtggcatatgctttgcatattttggcatgacttgataagttactccgcaaccttgtt-tggtctgatgggctgccctttacaataccacagATAGGCTATCTGGTGTCATGGATGATCGTGGGAAGTTCATATACATATCTACTGAGGAGATGAAGGCTGTCGCAGATTACATCAGGAAACAAGGGAGGGT
| ||| || | | ||| || ||| | ||| | ||| | | |||||||| ||||| ||||| ||||||||||| ||||| ||| | ||||| ||||| || || || |||||||| | | | |||| || ||
--------------------------------------------------------------------------------------------gtgagtctctttgtttctgcgttgtgctcttgaaaagag---tttgaggttttccagGGCGATTGTCTGGTGTGATGGACGATCGAGGGAAGTTCATTTACATCTCTCCGGAGGAAATGAAAGCGGTGGCGGATTACATAAAGCGAGAAGGCAGAGT
upper sequence: LOC_Os07g01320.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ24424 (Selaginella moellendorffii), 3'ss of exon 7
gtatgtatcactcttttgtgacttgaaactattgtcttgtgctactgcatcagcctaagtggcatatgctttgcatattttggcatgacttgataagttactccgcaaccttgtttggtctgatgggctgccctttacaataccacagATAGGCTATCTGGTGTCATGGATGATCGTGGGAAGTTCATATACATATCTACTGAGGAGATGAAGGCTGTCGCAGATTACATCAGGAAACAAGGGAGGGT
| ||| || | | ||| || | | ||| | ||| | | |||||||| ||||| ||||| ||||||||||| ||||| ||| | ||||| ||||| || || || |||||||| | | | |||| || ||
--------------------------------------------------------------------------------------------gtgagtctctttgttttttcgttgtgttc--ttgaaaagagtttgaggttttccagGGCGATTGTCTGGTGTGATGGACGATCGAGGGAAGTTCATTTACATCTCTCCGGAGGAAATGAAAGCGGTGGCGGATTACATAAAGCGAGAAGGCAGAGTMapped 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|218503102|gb|FG960043.1|FG960043EST: GACTGTATCAACCGGATCATTACACTTGAAGGCATGG ATAGGCTATCTGGTGTCATGGATGATCGTGGGAAGTTCATATACATATCTA
genomic: GACTGTATCAACCGGATCATTACACTTGAAGGCATGGgtatgtatca ... aataccacagATAGGCTATCTGGTGTCATGGATGATCGTGGGAAGTTCATATACATATCTA
EST:
gi|88958640|gb|CI096156.1|CI096156EST: GACTGTATCAACCGGATCATTACACTTGAAGGCATGG ATAGGCTATCTGGTGTCATGGATGATCGTGGGAAGTTCATATACATATCTA
genomic: GACTGTATCAACCGGATCATTACACTTGAAGGCATGGgtatgtatca ... aataccacagATAGGCTATCTGGTGTCATGGATGATCGTGGGAAGTTCATATACATATCTA
EST:
gi|29687912|gb|CB684187.1|CB684187EST: GACTGTATCAACCGGATCATTACACTTGAAGGCATGG ATAGGCTATCTGGTGTCATGGATGATCGTGGGAAGTTCATATACATATCTA
genomic: GACTGTATCAACCGGATCATTACACTTGAAGGCATGGgtatgtatca ... aataccacagATAGGCTATCTGGTGTCATGGATGATCGTGGGAAGTTCATATACATATCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagttactccgcaaccttgtttggtctgatgggctgccctttacaataccacagATAGGCTATCTGGTGTCATGGATGATCGTGGGAAGTTCATATACATATCTACTGAGGAGATGAAGGCTGTCGCAGATTACATCAGGAAACAAGGGAGGGT
gtctgat putative branch site (score: 4)
tttacaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatcactcttttgtgacttgaaactattgtcttgtgctactgcatcagcctaagtggcatatgctttgcatattttggcatgacttgataagttactccgcaaccttgtttggtctgatgggctgccctttacaataccacagATAGGCTATCTGGTGTCATGGATGATCGTGGGAAGTTCATATACATATCTACTGAGGAGATGAAGGCTGTCGCAGATTACATCAGGAAACAAGGGAGGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT