Sequence
atgc intronic sequence ATGC exonic sequencegtgagatttcgttttgttctttcctttttctctaactctcttgggctgggatcgttcatcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
Basic information
| species | Selaginella moellendorffii |
| transcript | EFJ11645 |
| intron # | 1 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 1
------------------------------------gtgagatttcgttttgttctttcctttttctctaactctcttgggctgggatcgttcatcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
| || | ||| || | | |||| | | || | | | ||||||||| ||||| || || ||||| |||||||| ||||| || || || ||||| ||||| |||||||| ||||| ||||||||||| |
agttctgtaacagtaggattcacctcattttgtatcttatgaatcggttgtgccttgagacgatatgtgcactcattgttcgcgtcattgctt-ttgacagGATTATGTTCCGACGGTGTTTGACAACTTCAGTGCCAACGTCGTGGTTGATGGTAACACCGTCAACCTCGGGCTATGGGACACTGCAG
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 1
-----------------------gtgagatttcgt-tttgttctttcctttttctctaactctct-tgggctgggatcgttcatca----------acagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
| | | | | | | | | || | || | ||| | | | ||||| ||| ||| |||||| || ||||| |||||||||||||||||||| || ||||| || |||||||| | |||||| ||| | ||| | ||||| || || |
tcgttttgtgcgaaaaaataaatctaatgtattgcatctttgcatttttaattggcagactgtatgtttaatgggacatttcttcatctctatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 1
------------------------------gtgagatttcgttttgttctttcctttttctcta----actctcttgggctgggatcgttcatcaac-agGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
| || || ||| | || | | | ||| || | | || | || | | |||| || ||||| || || |||||||||||||| ||||| || || || ||||| || ||||||||||| || |||||||||||||| |
ctcccactgtcctttgcctatttttctggtttatgaattagttgcacttttagtgatacatgcagtacacttactgttgtcgccattgctcttttgccagGACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGATGGTAATACTGTCAACCTCGGCCTCTGGGACACTGCAG
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM5G803949_T01 (Zea mays), 3'ss of exon 1
--------------------------------gtgagatttcgttttgttctttcctttttctctaactct--cttgggctgggatcgttcatca-acagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG------------
| || || ||| | || | ||| || || || | | || | || || ||||| || ||||| || || ||||| |||||||| || || || || || ||||| |||||||||||||| || |||||||||||||| |
ctctcccgttgtcctctgcccatttttctggtttatgaattagttgcacttttagtgatatctaggacacttactgctgtcgacattgctcttctcgcagGACTATGTTCCGACGGTGTTTGACAACTTCAGTGCTAACGTTGTGGTTGATGGTAACACTGTCAACCTCGGCCTCTGGGACACTGCAGGTGACTAGCCGT
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM5G803949_T03 (Zea mays), 3'ss of exon 1
--------------------------------gtgagatttcgttttgttctttcctttttctctaactctcttgg--gctgggatcgttcatca-acagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
| || || ||| | || | ||| || || | | | || | || || ||||| || ||||| || || ||||| |||||||| || || || || || ||||| |||||||||||||| || |||||||||||||| |
ctctcccgttgtcctctgcccatttttctggtttatgaattagttgcacttttagtgatatctaggacacttactgctgtcgacattgctcttctcgcagGACTATGTTCCGACGGTGTTTGACAACTTCAGTGCTAACGTTGTGGTTGATGGTAACACTGTCAACCTCGGCCTCTGGGACACTGCAG
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA01G36880.4 (Glycine max), 3'ss of exon 1
----------------------------------gtgagatttcgttttgttctttccttt--ttctctaactctcttgggctgggatcgttcatcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
|| ||| || || | || || | | | | | ||| | | || || | |||||||||| || || ||||||||||| || |||||||| |||||||||||| |||| | || ||| || || || | ||||| |||||||
tattatttattatgaagtttggttaacgttttttgttttgttttgtaatgagcatttggttaactatttgattacgttgtatttgtat-atttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA01G36880.2 (Glycine max), 3'ss of exon 2
----------------------------------gtgagatttcgttttgttctttccttt--ttctctaactctcttgggctgggatcgttcatcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG------------
|| ||| || || | || || | | | | | ||| | | || || | |||||||||| || || ||||||||||| || |||||||| |||||||||||| |||| | || ||| || || || | ||||| |||||||
tattatttattatgaagtttggttaacgttttttgttttgttttgtaatgagcatttggttaactatttgattacgttgtatttgtat-atttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGGTAATGCTGCGT
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 2
-----------------gtgagatttcgttt-tgttctttcctttt----------tctctaactctcttgggctgggatcgtt-------catcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
| | ||| ||| ||| ||| || | | || | | | || | ||| | |||||||||| || || ||||||||||| || ||||| || |||||||||||| |||| | || ||| || || || | ||||| |||||||
gtctcattttgtttattataaagtttggttaacgttttttttttataaacattaggttaacaatttgataacgttgtatttgttgtgtatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT4G35020.3 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------gtgagatttcgttttgttctttcctttttctctaactctcttgggctgggatcgttcat-caacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
|| || | | || ||| |||| | | || | ||| || | || ||||||||| || || ||||| || ||||| ||||| ||||||||| |||| |||||||||||| ||||| | || | ||||| ||||| |
aatgttgttgatctgtttaatgatcttagaaagagtgttaggtaactttctgtaaggagattttgtagctgatgttttag--tggaattttctatgtgacagGATTATGTGCCAACTGTGTTCGATAATTTCAGTGCCAATGTGATTGTTGATGGCAACACTATCAACTTGGGATTGTGGGATACTGCAG
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------------------------------------------------------------gtgagatttcgttttgttctttcc----ttttt----ctctaactctc-ttgggctgggatcgttcat---caacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
|||| ||||| | || ||| | || | |||| ||| | ||||| |||||||||| || || |||||||| |||||||| ||||| ||||||||||| |||| |||||| || |||||||| ||||| || || |
gtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatgaatcgatccataatttttttttggtgttatgaggatttgtggagctttgtatctcattgaatcttgtaaattcatgtggaacagGATTATGTACCGACTGTTTTCGATAACTTTAGCGCAAATGTGGTTGTTAATGGAGCCACTGTGAATCTTGGGCTATGGGATACCGCAG
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------------------------gtgagatttcgttttgttctttcctttttctctaactctcttgggctgggatcgtt-----catc--------aacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
| |||| | || || | | | | | | || | ||| ||| |||||||||| ||||| |||||||| |||||||| || || ||||||||||| |||| ||| || || ||||| | ||||| ||||| |
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgatt-gtgccatatatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv10s0003g00570.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------gtgagatt-tcgttttgttctttcctttttctctaact---ctcttgggctgggatcgttcatcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
|||| | ||| || | ||| |||| || | | | ||||||| |||||||| ||||| || |||||||| || || |||||||| ||||| | ||| ||||||||||| || ||||||||||| |
gtacgatttcatgtatatcaagtcatattcaagataattgttatggcagtgagcagagggataatggggttctttttcttaccttcccttttgatagGATTATGTTCCCACAGTTTTCGACAACTTCAGTGCTAACGTGGTTGTGGATGGTAGCACAGTCAACCTTGGCCTATGGGACACTGCAG
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv18s0001g14670.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------------gtgagatttcgttttgttctttcctttttctctaactctcttgggctgggatcgttcatca--acagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
|| | || | | | | || |||| | | | ||| | || ||||||||| || || ||||||||||| || ||||| || ||||||||||| ||||| | ||||||||| | ||| | ||||| |||||||
ctttggagttattcctcatttccataactgtatttggggagaaaagttactaactatgtgtgtcaacacattcttctgttctcaatgttgaccaaaacagGATTATGTGCCAACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTTGATGGGAGCACTGTCAATTTAGGGTTGTGGGATACTGCTG
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
----------------------gtgagatttcgttttgttctttcctttttct-------------ctaactctcttgggctgggatcgttcatcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
|| |||| | |||||| ||| | | || | | | || | | || || |||||||||| || || |||||||| || || ||||| || |||||||||||| |||| |||||| ||||||||| | ||||| |||||||
gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttctttgataggcaaaggacttattgttttatttttgaattattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S165_55V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------gtgagatttcgttttgttctttcctttttctctaac--tctcttgggctgggatcgttcatcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
| | | || || ||| |||||| ||| | ||| || | |||||||||||||| || |||||||||||||||||||| ||||| ||||||||||| |||||||| |||||||| || ||||| || || |
aacgctgtgatgtatatatatatatatatatatatatatccttttcttattatttaatttttcctgggtgacatctcaagagttaatccttattttgcagGATTACGTTCCTACCGTTTTTGATAACTTCAGCGCGAATGTCGTTGTCGATGGAAACACTGTAAACCTTGGACTATGGGATACAGCAG
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S51_114V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------gtgagatttcgttttgtt-ctttcctttttctctaac--tctcttgggc-tgggatcgttcatca-acagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
|| | ||| | | ||| | |||| || | || | || | ||||| | |||||||||||||| || || ||||| ||||||||||| ||||| || |||||||| || || |||||||| ||| | ||||| || || |
agggatggcgcgcaaggagatgtactttaccacagcgtctgttagacagcgcttcttgtactcttacgatgtcctaagcacatgcccgttcgtttcgcagGATTACGTTCCTACCGTGTTTGACAACTTCAGCGCAAATGTAGTGGTCGATGGAAATACCGTCAACCTCGGGTTATGGGATACAGCAG
upper sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S257_74V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------gtgagatttcgttttgttctttcc-----tttttctctaactctcttgggctg------ggatcgttcatca-acagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
|||| | | |||||||| | | | | || | ||||| ||| | ||| || |||||||||||| || ||||| || || ||||||||||| ||||| || |||||||| || || |||||||| || || ||||| || || |
ttctaacagaggcgtggacacgcgtgatgatatggcatgttctttgtatggaccactgttgcattttccttggctgaaaaatggaactttcgtctcacagGATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGATGGGAATACCGTCAACCTGGGACTATGGGATACAGCAGMapped 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|169057946|gb|FE465544.1|FE465544EST: TGGGCAAGACTTGCATGCTCATTTCATACACGAGCAACACTTTCCCCACT GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGAT
genomic: TGGGCAAGACTTGCATGCTCATTTCATACACGAGCAACACTTTCCCCACTgtgagatttc ... tcatcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGAT
EST:
gi|169057947|gb|FE465545.1|FE465545EST: TGGGCAAGACTTGCATGCTCATTTCATACACGAGCAACACTTTCCCCACT GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGAT
genomic: TGGGCAAGACTTGCATGCTCATTTCATACACGAGCAACACTTTCCCCACTgtgagatttc ... tcatcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGAT
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),
35 (downstream exon)
Score:
12CATGAGCACTTCAAGATTTATCAAGTGCGTTACCGTCGGAGATGGTGCGGTGGGCAAGACTTGCATGCTCATTTCATACACGAGCAACACTTTCCCCACTgtgagatttc ... tcatcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttgttctttcctttttctctaactctcttgggctgggatcgttcatcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG
ctctaac putative branch site (score: 12)
tttttct TA-rich tract
