Sequence
atgc intronic sequence ATGC exonic sequencegtgcgttttttagttttgttatacgtccttctaacatttttctacagGAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ37641 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ37641 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G129155_T02 (Zea mays), 3'ss of exon 9
---------------------------gtgcgttttttagttttgttatacgtccttctaacatttttc--tacagGAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAG
| ||| | || |||| | ||| | || || | || |||||||||||||||| ||||| ||| | || |||||||||||||| | || ||||||||||| |||||||| | || || ||||||||| || ||
gtgcgtaactggacagtggttttcatcatatgttgataagcgttgtcacgagtctattaaatatatatcattacagGAGGTTGATCCTTGTGAGGATGTTACAGATGAAGATATCCGCATGGCTATTCAAAATGCAACTGGTCCTAGAAGTGCTCTGTTTGTACCTGAA
upper sequence: EFJ37641 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA07G30150.1 (Glycine max), 3'ss of exon 9
---------------------------------------------------gtgcgttttttagttttgttatacgtccttctaacatttt--tctacagGAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAG
| | | | ||| | ||||| ||| ||||| |||||||||| ||||||||||| ||| |||||||||| ||||| || |||||||| || ||||||||||| || ||| | |||||||| || ||
tcactccattgaaccacccaatgatcatgttcctctgttcatttcttcaatgctagctcctgagtcctattatataatgcaataaaattttatcttacagGAGGTGGATCCATGTGAAGATTTGACTGATGATGATATTCGCACAGCCATACAGAATGCCACTGGACCTAAATCAGCACTGTTTGTTCCAGAA
upper sequence: EFJ37641 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 9
------------------------------------------------gtgcgttttt-tagttttg---ttatacgtccttctaacatt-tttctacagGAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAG
||| | | | || ||| | || | ||||| ||| ||||||||||||||||| || || |||| ||||| ||||| || || || ||||| ||||| |||||||||| | || | ||||| || ||
gacattatccaaatggaaataatgtagtatatttctgacgttgagctcgtggatctctgtaaatttagactgattgaattccttcacattgcctcttcagGAGGTTGATCCATGCGAGGACTTGACAGATGATGATATTCGGACTGCAATTCAGAATGCAACTGGTCCAAGATCTGCATTATTTGTTCCAGAT
upper sequence: EFJ37641 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 10
---------------------------------------gtgcgttttttagttttgttatacgtccttctaac--------------atttttctacagGAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAG
||| ||| || || ||| | | || | || | | | |||||||| ||||||||||| ||| |||||||||| || || ||||| || ||||| ||||| || || || | | || | |||||||| ||
atggagaacctcacaattttttattggtaaatctgatgtttgctaatttcagagctgctatgagctcatcaagtctgaggagatttgaatatctgtgcagGAGGTGGATCCATGTGAGGATTTGACTGATGATGACATTCGAACTGCAATTCAGAATGCAACCGGCCCTAGATCTGCATTATTTGTGCCAGAAMapped 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|169045738|gb|FE453050.1|FE453050EST: GAGCTCGTATTCACTACATATTCCAATCAATTTTCGTCAAAAGCTTAGAC GAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATT
genomic: GAGCTCGTATTCACTACATATTCCAATCAATTTTCGTCAAAAGCTTAGACgtgcgttttt ... ttttctacagGAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATT
EST:
gi|169096017|gb|FE500008.1|FE500008EST: GAGCTCGTATTCACTACATATTCCAATCAATTTTCGTCAAAAGCTTAGAC GAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATT
genomic: GAGCTCGTATTCACTACATATTCCAATCAATTTTCGTCAAAAGCTTAGACgtgcgttttt ... ttttctacagGAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATT
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:
23 (upstream exon),
28 (downstream exon)
Score:
5AGTTGTGGATGGCAAAAACGAAGAGATGTCAACTGTTGAACTATCTGGGGGAGCTCGTATTCACTACATATTCCAATCAATTTTCGTCAAAAGCTTAGACgtgcgttttt ... ttttctacagGAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgcgttttttagttttgttatacgtccttctaacatttttctacagGAGGTTGATCCATGTGACGATCTGACTGATGAAGATATCCGAACAGCCATTCAAAATGCCACTGGTCCAAAAAATGTTCTGTTTGTGCCCGAG
ttctaac putative branch site (score: 5)
catttttct CT-rich tract
ttttttagttttgtta TA-rich tract