Sequence
atgc intronic sequence ATGC exonic sequencegttcctcaaactctgtttgaaactctgtaatcattccgtttcgctgcagCTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGGTATTTAGCGCCAATGACAGCACTATCACGGAGGAAGATATTGATCGCAT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ06565 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
--------------------------gttcctcaaactctgtttgaaac-tctgtaatcattc------cgtttcgctgcagCTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGGTATTTAGCGCCAATGACAGCACTATCACGGAGGAAGATATTGATCGCAT
| | |||| || |||| || | | ||| ||| | | |||||||||| || |||||||| ||||||||||| |||||||| || || |||||||| ||| |||| || ||||| || || || ||||||||||| |||||
gttagttttttgcttcataaaatgttgcttgacaaatgaaaattcaaacatcaattaatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
upper sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
-----------------------------------gttcctcaaactctgtttgaaactctgtaatcattccgtttcgctg-cagCTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGGTATTTAGCGCCAATGACAGCACTATCACGGAGGAAGATATTGATCGCAT
| ||| | | | || | || | | ||| ||| || |||||||||| || ||||| || ||||| |||||||||||||| ||||| |||||||| || |||| |||||||| || || || || |||||||| || ||
gtatgtttttgctgcttgtattttatgtttaagaaggcattcatgcagtagt--aagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT
upper sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 13
-----------------------------------------------gttcctcaaactctgtt---tgaaactctgtaatcattccgtttcgctgcagCTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGGTATTTAGCGCCAATGACAGCACTATCACGGAGGAAGATATTGATCGCAT
||| | |||| | | | | ||| | || | ||||||||| |||||||||||||| |||| ||||| || ||||| || || ||||| || ||| |||| || ||||| || ||||| ||||| || || | ||
gtgagccatttctgcattacaagcttgctttgcactatgacatgctaattcatagaactagaaccactaacattttgttgtttttgtgggcttttgcagCTGTGAACAAAGATGAGCTACTGCAAATGGTCAGGTTTGGTGCTGAAATGGTTTTCAGCTCCAAGGATAGCACAATTACGGATGAAGACATAGACAGGATMapped 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|169107316|gb|FE504142.1|FE504142EST: TGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCTGAACAGAGAG CTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGG
genomic: TGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCTGAACAGAGAGgttcctcaaa ... ttcgctgcagCTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGG
EST:
gi|169028023|gb|FE435914.1|FE435914EST: TGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCCGAACAGAGAG CTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGG
genomic: TGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCTGAACAGAGAGgttcctcaaa ... ttcgctgcagCTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGG
EST:
gi|169023478|gb|FE430076.1|FE430076EST: TGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCTGAACAGAGAG CTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGG
genomic: TGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCTGAACAGAGAGgttcctcaaa ... ttcgctgcagCTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGG
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:
33 (upstream exon),
12 (downstream exon)
Score:
4TATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCTGAACAGAGAGgttcctcaaa ... ttcgctgcagCTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGGTATTTAGCGCCAATGACAGCACTATCACGGAGGAAGATATTGATCGCAT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcctcaaactctgtttgaaactctgtaatcattccgtttcgctgcagCTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGGTATTTAGCGCCAATGACAGCACTATCACGGAGGAAGATATTGATCGCAT
ttccgtttc CT-rich tract
taatcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcctcaaactctgtttgaaactctgtaatcattccgtttcgctgcagCTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGGTATTTAGCGCCAATGACAGCACTATCACGGAGGAAGATATTGATCGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA