Sequence
atgc intronic sequence ATGC exonic sequence...ccttggtattaatatcatgtcaatctaaagaggatgttatgggtatattttttatttaataggattttatgctgtcagttgttccttaagaaaaccatagGCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGATGGTTATTTGGATGATGACTATCTTGTGTTTGATTGCCCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g21914.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G131324_T01 (Zea mays), 3'ss of exon 4
ccttggtattaatatcatgtcaatctaaagaggatgttatgggtatattttttatttaat-aggattttatgctgtcagttg----ttccttaagaaaaccatagGCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGATGGTTATTTGGATGATGACTATCTTGTGTTTGATTGCCCAG
| ||| |||| ||||| || | | ||||| || | ||| ||| | ||||||||||||| |||||| |||||||| |||||| |||||||||||||||| |||||||||||||| ||||| || || || || | |||||||| |||||||||||||||||||| |
acaatgtaataat-tcatgaagat----attgttccttatgttcatggtgtttgttttgttaggattttatgctttcagtttctgtttccttaacaaaacctcagGCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTACCTAGATGATGATTATCTTGTGTTTGATTGCCCTG
upper sequence: LOC_Os03g21914.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G154716_T01 (Zea mays), 3'ss of exon 6
ccttggtattaatatcatgtcaatctaaagaggatgttatgggtatattttttatttaataggattttatgctgtcagttg----ttccttaagaaaaccatagGCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGATGGTTATTTGGATGATGACTATCTTGTGTTTGATTGCCCAG
| | ||| | ||| |||||||||||||| ||| || |||||||| |||||| |||||||||||||||| |||||||||||||| ||||| || || || || || |||||||| |||||||||||||||||||| |
-------------------------------------------tggagtttgt-tttgttaggattttatgctttcattttctgtttccttaacaaaacctcaggcaccttgaagacagcttggatgattggtttgatgaacagCTAGAGAACTACTTAGATGATGATTATCTTGTGTTTGATTGCCCTG
upper sequence: LOC_Os03g21914.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv00s0174g00200.t01 (Vitis vinifera), 3'ss of exon 3
----------ccttggtattaatatcatgtcaatctaaagaggatg-----ttatgggtatatttttta-----tttaataggattttatgctgtcagttgttccttaagaaaaccat-agGCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGATGGTTATTTGGATGATGACTATCTTGTGTTTGATTGCCCAG
|||| | ||| | || | || |||| | | || | | | || || ||| | |||| | | | | | | | || |||||||||||||| ||||||||||||||||| || || ||||| ||| ||||||||||||||| | |||||||| |||||||
gtatccttttcctttgcattttatttatttgtatttaaatatttttcatccttttagatgatgttgctagttgtttttgcgaaggtgtatgttttgaatgaccttacatctcagcaattagGCACCTTGAAGAAAATTTGGATGATTGGTTAACAGATGAATTGGATAATTACTTGGATGATGACTATTTGGTGTTTGACTGCCCAGMapped 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|58656588|gb|CK045268.1|CK045268EST: ATGGAGGAACTTGGGATGGGACCAAATGGCGGGCTTATCTATTGCATGGA GCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGATGGTTA
genomic: ATGGAGGAACTTGGGATGGGACCAAATGGCGGGCTTATCTATTGCATGGAgtatcctgtt ... aaaaccatagGCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGATGGTTA
EST:
gi|27546018|gb|CA764157.2|CA764157EST: GGGACCAAATGGCGGGCTTATCTATTGCATGGA GCACCTTGAAGACAATTTGGATGGTTGGTTGGATGAGCAACTGGATGGTTA
genomic: GGGACCAAATGGCGGGCTTATCTATTGCATGGAgtatcctgtt ... aaaaccatagGCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGATGGTTA
EST:
gi|33679512|gb|CF307751.1|CF307751EST: ATGGAGGAACTTGGGATGGGACCAAATGGCGGGCTTATCTATTGCATGGA GCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGAGGGTTA
genomic: ATGGAGGAACTTGGGATGGGACCAAATGGCGGGCTTATCTATTGCATGGAgtatcctgtt ... aaaaccatagGCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGATGGTTA
EST:
gi|44673938|gb|CR287372.1|CR287372EST: CTTATCTATTGCATGGA GCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGATGGTTA
genomic: CTTATCTATTGCATGGAgtatcctgtt ... aaaaccatagGCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGATGGTTA
EST:
gi|58671472|gb|CK060158.1|CK060158EST: ATGGAGGAACTTGGGATGGGACCAAATGGCGGGCTTATCTATTGCATGGA GCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGAGGGTTA
genomic: ATGGAGGAACTTGGGATGGGACCAAATGGCGGGCTTATCTATTGCATGGAgtatcctgtt ... aaaaccatagGCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGATGGTTA
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:
68 (upstream exon),
68 (downstream exon)
Score:
14ATATTAGGGAGCTCATATCATTGGATGATGTCATGGAGGAACTTGGGATGGGACCAAATGGCGGGCTTATCTATTGCATGGAgtatcctgtt ... aaaaccatagGCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGATGGTTATTTGGATGATGACTATCTTGTGTTTGATTGCCCAG
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattttttatttaataggattttatgctgtcagttgttccttaagaaaaccatagGCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGATGGTTATTTGGATGATGACTATCTTGTGTTTGATTGCCCAG
ttccttaag putative branch site
tttatttaataggatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccttggtattaatatcatgtcaatctaaagaggatgttatgggtatattttttatttaataggattttatgctgtcagttgttccttaagaaaaccatagGCACCTTGAAGACAATTTGGATGATTGGTTGGATGAGCAACTGGATGGTTATTTGGATGATGACTATCTTGTGTTTGATTGCCCAG
- - - - - - -atcatgt
- - - - - - - - - - - - - aaagagga
- - - - - - - - - - - - - - - - - tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgtc