Sequence
atgc intronic sequence ATGC exonic sequencegtatcttgtttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g01380.1 |
intron # | 28 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 26
gtatcttgt---ttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagctt------------gcttcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
||| | || ||| || ||||| || | |||||| ||||||| ||||| |||| || || ||| |||||||||||| || ||||| |||||||| ||||| |||||||||||| ||| || || ||||| |||| ||| || || |||||||| || ||||| ||||
gtacgtagtaatttctgtccatgttcgtgccgacgtctatttacatacagtttaccatagtaacatctctactgtgctatgtgactgtgtgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCCAAGGAGAAGGAGGAGAAAGACCTTG
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM2G115138_T01 (Zea mays), 3'ss of exon 12
gtatcttgt---ttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagctt------------gcttcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
||| | || ||| || ||||| || | |||||| |||||| ||||| |||| || || ||| |||||||||||| || ||||| |||||||| ||||| |||||||||||| ||| || || ||||| |||| ||| ||||| |||||||| || ||||| ||||
gtacgtagtaatttctgtccatgttcgtgccgacgtctatttacatacagtta-ccatagtaacatccctactgtgctatgtgactgtgtgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 5
gtatcttgtttccgttcatgtgtt-tgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
||| ||| ||| || ||| | | || | || |||| | | | ||| | || |||| | |||| |||||||||||||| || || ||||| |||||||| ||||| ||||||||||||| ||||| ||||||||||||| ||| | ||||||||||| || ||||||||||
gtaacttacttctgtccatatctgacggtgatgtttgtttatgtataatttactatggtaacatc-catgctgcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTG
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 13
gtatcttgt---ttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
||| | || || || ||||| | | |||||| ||||||| ||||| |||| | | || ||| |||||||||||| || ||||| |||||||| ||||| |||||||||||| ||| || || ||||| |||| ||| ||||| |||||||| || ||||| ||||
gtacgtagtaatttttgtccatgttcgcgccgacgtctatttacatacagtttaccatagtaacatc-cctactatgtgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 5
----gtatcttgtttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttg--cttcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
|| ||| |||| | | | | ||| | || ||||| | ||||| | || || || || |||||||||||||| || || ||||| |||||||| ||||| |||||||||||| || || ||||||||||||| ||| || ||||||||||| || ||||||||||
gtaactaacttatttctgcccgtacctgtggtgatgtttgtttacatatagtttactatggtaataacatccatcctgcgtgtgcagTTCATCCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATCGAGTCACAGAATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTG
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 8
gtatcttgt---ttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagctt------------gcttcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
||| | || ||| || ||||| || | |||||| | |||| ||||| |||| || || ||| |||||||||||| || ||||| |||||||| ||||| |||||||||||| ||| || || ||||| |||| ||| ||||| |||||||| || ||||| ||||
gtacgtagtaatttctgtccatgttcgtgtcgacgtctatttacatatagtta-ccatagtaacatccctactgtgctatgtgactgtgtgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 13
gtatcttgt---ttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagct----tgcttcgtg--------tgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
||| | || ||| || ||||| | | | |||| |||||| ||||| |||| || |||| ||| |||||||||||| || ||||| |||||||| ||||| |||||||||||| ||| || || ||||| |||| ||| ||||| |||||||| || ||||| ||||
gtacgtagtaatttctgtccatgttcgcgccgacgtctacttacatacagtta-ccatagtaacatccctactgtgctatgtgactgtctgcgcagTTCATTCGTGAATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTG
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 28
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 28
-------gtatcttgtttccgttcatgtgtttggga-----ctattcatt-------tacgaacagttttccataacaacaaagcttgcttcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
|| | | || | ||| || | ||||| ||| || | || |||| | | | | || | | || |||| ||||| |||||||| |||| || ||||| ||||||||||||| |||||| |||| |||||||| | |||||||||| | |||||||| ||| | |
agttattgtcttctccagccttccattgagctgaaatgaatctatttattgccatcttatccagaggtttctctcatcattattttttttggggttgtagTTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATTGAAGCACAAAATGAAGTGAAGGCTAAAGAGCAAGAAGAAAAGGATGTAGMapped 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|87030226|gb|CI270236.1|CI270236EST: CTATCTGTTACAG TTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
genomic: CTATCTGTTACAGgtatcttgtt ... tcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
EST:
gi|29685119|gb|CB681394.1|CB681394EST: TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAG TTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAACGACATGATT
genomic: TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtt ... tcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
EST:
gi|29627717|gb|CB632728.1|CB632728EST: TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAG TTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
genomic: TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtt ... tcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
EST:
gi|29626374|gb|CB631385.1|CB631385EST: CATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAG TTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
genomic: CATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtt ... tcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
EST:
gi|29624173|gb|CB629184.1|CB629184EST: TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAG TTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
genomic: TTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtt ... tcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
72 (upstream exon),
75 (downstream exon)
Score:
191TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtt ... tcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
ccataac putative branch site (score: 191)
cttgcttc putative PPT
attcattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcttgtttccgttcatgtgtttgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA