Sequence
atgc intronic sequence ATGC exonic sequencegtatgcacatttttccttcttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ37833 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
----------------------gtatgcacatttttccttcttgaccggtgtaa--gaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
| || | | || | | | ||| ||| | | |||||||||||| ||||||||||||| || |||||| |||| || | || ||||||||||||||||| ||||||||||| ||||||||||||||||| || |
gtaaatgctcaatatcttttttggataaatacttcaaaattcaggaaattttaattatgcttccttcatgcagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA
upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: LOC_Os08g06480.1 (Oryza sativa), 3'ss of exon 20
------------------------------------------------------------------------gtatgcacatttttccttcttgaccggtg----taagaacttgccatgtc----cagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
|| | || | | |||| | ||| ||| | || || | ||||| ||||| | |||||| |||| ||||| || ||||| ||||| || || |||||||||||||| |||||||| || ||||||||||| || ||||| |
gtatatgatctcttcggtgtgtagcacaatcaattgttattaccctagagcataggtcatgagttactttccataaaaatatgtgttattctatagttgtgacgttaaaatttttgaattttttcacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCTCAAGACAATAATATCATTGCTATTGGAATGGAGGACTCTACCA
upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 21
-------------gtatgcacatt-tttccttcttgaccggtgtaagaactt--gccatgtc-------cagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
||| ||| ||| |||| | |||||| ||| | ||| ||||||| | || ||||| ||||| || || |||||||| || ||||| || |||||||| ||||| || ||||| ||||||||||| || || || |
gttagttacaagtttatttctattgtttgtctcttatgtagaaattgaactttaatcatatggtgactgcagACGATGACAACTTTTATGCCTCCGCCGCCGGCGGCAACGTTTCTTGCTTTCCATCCTCAAGATAACAACATTATAGCAATTGGAATGGATGACTCAACCA
upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
-----------------------------------gtatgc-acatttttccttcttgaccggtgtaagaacttgccatg---------------tccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
|| || ||| | |||||| || | | | ||| | | |||||||||||| ||||||||||||| ||||||||| |||| || | || ||||||||||||||||| || |||||||| || |||||||||||||| || |
atctataagcaggtcattagatgcttatataatccataagctggattatataatcttgagaggaaacaaacatggccttaatcatgcatccttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
----------------------gtatgcacatttttccttcttgaccggtgtaa--gaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
||| | ||| || | | ||| | | | | |||||| ||||| |||||||||| || ||||||||| |||| || | || |||||||||||||| || || |||||||| || |||||||||||||| || |
gtaatgtctaactgttttattctgatgaaattttcagatttcaagaagatttaatcatgcatccttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GRMZM2G042992_T01 (Zea mays), 3'ss of exon 20
---------------------------------------------------------------------------------------------------------------gtatgcacatttttcc----ttcttgacc-ggtgtaagaacttgccatgtc---cagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
| | ||| || | ||||| || | | | || || || ||||| ||||| | |||||| |||| ||||| || ||||| ||||| || || ||||| ||||| || |||||||| || ||||||||||| || ||||| |
gtagatgtccttttcagcgcctcaccataattttgttcgtctcatagatgtccatgagtcaatggtagttgtagtttgctgctgatagcttcagataaaaattgttataccatgatcgcatcattgccaatttcttaccctaaagcttggatctgggatctctgacagGTCATGACTACTTTCATGGCACCTCCACCTGCTGCAACTTTCCTTGCATTCCACCCACAAGATAATAATATCATCGCCATTGGAATGGAGGACTCTACCA
upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 20
------------------------------------gtatgcacatttttccttcttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
| | | | || | || | | ||||| |||||| ||||||||||||| || || || | || || |||||||| ||||||||||| ||||| |||||||| ||||| ||||| ||||| ||||
gtacatgtccagagatacaagtacaaccattacattccgttccgctgctatgttttctgtttacttatggtttattttctatcagGTAATGACAACATTCATGCCACCACCCCCTGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAA
upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 21
----------------------------gtatgcacatttttccttcttgaccggtgtaagaacttgccatgt-ccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
| ||| | || | || | | ||||| |||||| ||||||||||||| ||||| || | || || || ||||| ||||||||||| || || |||||||| ||||| ||||| ||||| ||||
gtacatgtccagagatacaaccatgacattccatacagccgcaatgtttactgtatacttaggtttattttctatcagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA
upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GLYMA13G22720.1 (Glycine max), 3'ss of exon 21
------------------------------------------------------gtatgcacatttttccttc-ttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
|| | ||| | | | || | ||| ||| || || | ||| |||||| | ||||||||||| |||||||| || || || || || ||||| ||||||||||||||||| || || ||||| ||||| || ||| | |
cttttgatggtttagtttagtatttccagacctcagtatcattttttttgttgcaattgtatattgtggttacattaatttctgt--gaattt--caactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCA
upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: GLYMA17G12110.2 (Glycine max), 3'ss of exon 21
------------------------------------------------------gtatgcacatttttccttc-ttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
|| | ||| | | | || | ||| ||| || || | ||| |||||| | ||||||||||| |||||||| || || || || || ||||| ||||||||||| ||||| || || ||||| ||||| || ||| | |
ccttttgatggtttggtttagtatttccagaccttagtatcatttttttgttgcaattgtatattgtggttacattaatttctgt--gaattt--caactgcagACAATGACAACTTTCATGCCACCTCCACCAGCTGCGACATTTCTTGCATTTCATCCTCAAGACAATAATATTATTGCTATTGGCATGGAGGACTCTTCCA
upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 20
-----------------------------------------------------------------------gtatgcacatttttccttcttgac--cggtgtaagaacttgccatgtc-cagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
||| | | ||| | | | | || |||| | ||||||||||| |||||||||| || ||||||||| ||||||| |||| || || ||||| ||||| || |||| || |||||||||||||| ||||| |
gtatatattatctatatgaacttaaaaaaagccacaagatttctaactgaaaatgttctcacactaatctagtaaactcttttggttgttctaatttccacaaaaaaactattggccttatagGTGATGACAACATTCATGCCGCCTCCACCAGCATCAACGTTTTTGGCGTTCCATCCTCAGGACAATAACGTCATCGCCATTGGAATGGAAGACTCTACGA
upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 20
------------------------------------------------------------------gtatgcacatttttccttcttgaccggtgtaaga---acttgccat----gtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
||| | | ||| | | || | | | | || | || ||||| |||||| | |||||||||||||||||||| |||| ||| |||| ||||| |||||||| || ||||| || || || || ||||| || || | |
gtaagcagcttaatccaactttttctgttctcgggagcatctcctaaatactgatacctcaggagctaatgaaactatttgagtaatatgcgaagctaaatgcatttttccctttcgtgcagGTAATGACAACTTTCATGCCACCGCCACCAGCTTCAACTTTCTTGGCATTTCATCCTCAAGATAATAATATTATTGCAATCGGGATGGAGGACTCGAGTA
upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
-----------------------gtatgcacat----ttttccttcttgaccggtgtaa---gaacttgc---catgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
| || ||| ||| | | | | ||| || || |||| ||| | |||| |||||| |||||||| |||| || || || |||| ||||| || || || ||||||||||| || |||||||| || |||||||| |||||||| |
gtatgtctaaacatcacagttttgcatcttcatcaaatttggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA
upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 21
---------------------------------------------------gtatgcacatttttccttcttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
|| |||||| |||| ||||| || |||||||||||||| || |||| || || ||||||||||| |||||||| || || || ||||| || ||| | |
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagACCATGACAACATTTATGCCCCCACCACCAGCAGCAACATTTTTGGCATTCCATCCTCAAGACAATAATATCATTGCCATAGGCATGGAGGACTCTTCTA
upper sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 20
-----------------------------------------------------------------------------gtatgcacatttttccttcttga--ccggtgtaagaacttgccat---gtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
| | ||| || || | || | | | | | | | ||||| ||||| ||||||||||||| || |||||||| || || || || ||||| || ||||||||||||||||| || || |||||||||||||| ||||
gtaaagtccgcgaatcatgaggagtctattttattctttgttctaataatatggtgagaagcgttttgtttttggtaattttgacagttgtcaatttttattctgacgcttttcttcggattttgactcagGTCATGACGACATTCATGCCACCACCTCCAGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAAMapped 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|169031531|gb|FE438996.1|FE438996EST: GTCCGCTTTCGG-AGGCAAAGTTTCTCTATTTAATATGATGACTTTCAAG GTGATGACAGCATTCATGCCCACCGC-ACCAGCAGCAACGTTCCTGGCTTT
genomic: GTCCGCTT-CGGGAGGCAAAGTTTCTCTATTTAATATGATGACTTTCAAGgtatgcacat ... ccatgtccagGTGATGACAGCATTCATGCC-ACCGCCACCAGCAGCAACGTTCCTGGCTTT
EST:
gi|169048259|gb|FE456246.1|FE456246EST: TGTCCGCTTCGGGAGGCAAAGTTTCTCTATTTAATATGATGACTTTCAAG GTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTT
genomic: TGTCCGCTTCGGGAGGCAAAGTTTCTCTATTTAATATGATGACTTTCAAGgtatgcacat ... ccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTT
EST:
gi|169026734|gb|FE436308.1|FE436308EST: TGTCCGCTTCGGGAGGCAAAGTTTCTCTATTTAATATGATGACTTTCAAG GTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTT
genomic: TGTCCGCTTCGGGAGGCAAAGTTTCTCTATTTAATATGATGACTTTCAAGgtatgcacat ... ccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTT
EST:
gi|169110734|gb|FE514183.1|FE514183EST: TGTCCGCTTCGGGAGGCCAAGTTTCTCTATTTAATATGATGACTTTCAAG GTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACG
genomic: TGTCCGCTTCGGGAGGCAAAGTTTCTCTATTTAATATGATGACTTTCAAGgtatgcacat ... ccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACG
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:
34 (upstream exon),
25 (downstream exon)
Score:
5GGAAGAAGCTGTGCCTTGCATTGCCTTGTCAAAGAATGACTCTTACGTGATGTCCGCTTCGGGAGGCAAAGTTTCTCTATTTAATATGATGACTTTCAAGgtatgcacat ... ccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatgcacatttttccttcttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
tcttgac putative branch site (score: 5)
acattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcacatttttccttcttgaccggtgtaagaacttgccatgtccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA