Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcgatcgatcaaaagccatctttttcttcgatatctccattgattggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ14420 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os11g06890.1 (Oryza sativa), 3'ss of exon 2
-----------------------------gtaagttcga--tcgatcaaaagccatctttttcttcgatatctccattgat-tggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| || | || || |||| || || | ||| | |||| | ||||| | || ||||||| ||||| |||||||| |||||||| || || ||||||||||| ||||| || || || || | || || || |||||||||||||| ||||||||
cctcggtgttcatgactaccctttgtgttgagagcttgaggctactcctaagctgcctactt--tggattacaattctgatatctcttgttggtgttggcagGGCAAATGCACAGCAACCAAAGCTTTTCGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCCCTGTATGGTCTCATTGTGGGCATCATCCTC
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
-------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctcca--ttgattggtttgtttttct---------ttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
|| ||| | | | | | || || | | | | || |||| || |||| || |||||||||||| || || || ||||||||||| || ||||||||||| ||||| || || || || | ||||| |||||||||||||| ||||| |||||
taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G028432_T01 (Zea mays), 3'ss of exon 1
-----------------------gtaagttcgatcgatcaa--aagccatcttttt---cttcgatatctccattgattggt--ttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| || ||| |||| || || | | ||| |||||| || ||||| || | |||||||||| || ||||| || ||||| ||||| || ||||||||||| |||||||| || || || | || |||||||||||||| || || ||||||||
cacttaaacacttgtcctacttgggaaaatcggattgtcaaccgggctggctgcctagacggcgacatctcctcatcctgacacttgttcttttgcgcagGGCGAACGCTCAGCAGCCAAAGCTGTTTGTGGGCATGATCCTCATCCTCATCTTCGCTGAAGCGCTCGCCCTATACGGTCTCATCGTCGGCATCATCCTC
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G177005_T01 (Zea mays), 3'ss of exon 2
----------------------------gtaagttcgatcgatcaaaagccatctt--tttcttcgatatctccattgattggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
|| ||| | | || ||| || || | | | ||| | | || |||||| |||||||| || || |||||||| ||||| ||||||||||| ||||| || || || || | ||||| || ||||| ||||| ||||| |||||
agtagctcacatgcaactttctcctggcgtttcttcttttacagaggaggcatgggaattgaaattttagtttgactaatttttgggccaccgatttcagGGCAAATGCGCAACAGCCAAAGCTTTTCGTTGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTCTATGGTCTAATTGTTGGAATTATCCTT
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA16G24220.1 (Glycine max), 3'ss of exon 2
----------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccat--tgattggtttgtttttcttt-gcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| | || | || || | || || || | | ||| | || ||||| |||| || ||||| ||||| || |||||||||||||||||||| ||||| ||||| ||||| ||||| ||||| |||||||||||||||| || ||||||||
atgcatttttagttcactcctgttgattatgaattt-actaatagtaatttaagcttcattttgacgaattgaatatgacatgccggtaactcttttgcagAGCAAATGCTCAGCAGCCAAAGCTTTTTGTTGGAATGATACTCATCCTCATTTTTGCTGAGGCGTTGGCATTATACGGTCTCATTGTTGGCATCATCCTC
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA12G04090.1 (Glycine max), 3'ss of exon 2
-------------gtaagttcgatcgatcaaaagccatctt-------tttct--tcga-----tatctcca---ttgattggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| |||| ||| || | | | | || || || | || || || | |||| ||| | || | ||||| || ||||| ||||| || |||||||||||||||||||| ||||||||||||||||| |||||| | || || || || |||||||| || || ||||||
tgtatattttgctgatagtttgatacatggatataccttttataatgattcctaatagaaattttaccttgaagtttgaacaatttatcttcttatgcagAGCCAATGCACAGCAGCCAAAGCTTTTTGTTGGAATGATTCTCATTCTCATCTTTGCTGAGGCTCTTGCCCTGTATGGACTCATTGTTGGTATTATCCTG
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA02G05630.1 (Glycine max), 3'ss of exon 2
----------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccat--tgattggtttgtttttcttt-gcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| | || | || | | || || | | | | ||| | | || ||||| |||| || ||||| ||||| || || ||||||||||||||||| ||||| ||||| ||||| ||||| ||||| |||| |||||||| || || ||||||||
acgtcatgttggttcactcctgttgattatgaattt-actaatggtattttaagcttaattttaacaaattgaatatgacttgccggtaactcttttgcagAGCAAATGCTCAGCAGCCTAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAGGCATTGGCATTATATGGTCTCATCGTTGGCATCATCCTC
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA11G07980.1 (Glycine max), 3'ss of exon 1
----------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccattgattggtttg--tttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| | ||| | | | | || | ||| |||| | | | || |||| || || ||||| || || || |||||||||||||| ||||| ||||||||||||||||| ||||| ||||| | || || |||||||| || ||||||||
acgctttgttaaccaagagattgttcaactcttactggatgattgtgtctaacttctattttagttattgaatttgacatgctgaaaatgttttttgtagAGCAAATGCCCAACAGCCAAAGCTTTTTGTTGGGATGATTCTCATTCTCATCTTTGCTGAGGCGTTGGCATTGTATGGACTCATTGTTGGCATCATCCTC
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA11G11760.1 (Glycine max), 3'ss of exon 2
---------------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccattgattggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| | ||| | || || || | || | | | |||| ||| | || | |||| || ||||| ||||| || |||||||||||||||||||| || |||||||| ||||| || ||| | ||||| || ||||||||||| || || ||||||
cattgatggttaattttatacagggatatagtttttataatgatattcctaataaaattcttattttgaagaagt---ttgaacaatttatcttcttccgcagAGCCAATGCACAGCAGCCAAAGCTTTTTGTTGGAATGATTCTTATTCTCATTTTTGCTGAAGCTCTTGCTCTCTATGGTCTCATTGTTGGTATTATCCTG
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA01G37320.1 (Glycine max), 3'ss of exon 1
---------------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccattgattggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
||| | | | ||| | || || | || | ||||| ||||||| || || || ||||| || || || |||||||||||||| ||||| ||||||||||||||||| ||||| ||||| | || || |||||||| || ||||||||
tttttaactgagagattgctcaactcttactggataaatgtgtttaatctcgattttagttattgaatatgacctgctgaaattggactgttttt---tgtagAGCAAATGCCCAACAGCCAAAGCTTTTTGTTGGGATGATTCTCATTCTCATCTTTGCTGAGGCGTTGGCATTGTATGGACTCATTGTTGGCATCATCCTC
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA04G00950.2 (Glycine max), 3'ss of exon 1
------------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccattgattggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| | | | || | | |||| ||| | | | ||||| | | | | ||||| || ||||| ||||| || || ||||||||||||||||| ||||| ||||| ||||| || ||| | || || || ||||| || || || || ||||||
gaacatatatctttttgcctttactagcatgcatttgttgtgaatttgacggtggattttccttttacaataatactgattaatcaatctgcttctgcagAGCCAATGCACAGCAGCCAAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAAGCTCTTGCCCTTTATGGTCTAATCGTTGGTATTATCCTG
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA06G00980.1 (Glycine max), 3'ss of exon 2
----------------------------gtaagtt-cgatcgatcaaaagccatctttttcttcgatatctccattgattg-gtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| ||| | || | |||| ||| | | | ||||| || | | | | ||| || ||||| || ||||| || ||||||||||||||||| ||||| ||||| ||||| || || | || || || ||||||||||| || || ||||||
atatatctttttgcctttactagcttgcatttgttgttgtgaatttgacagtggattttccttttacaataatactgattaagtcaatctacttctacagAGCCAATGCACAACAACCAAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAAGCACTTGCCCTTTATGGTCTCATTGTTGGTATTATCCTG
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT1G75630.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccattgattggttt----gtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| || ||| | | | | | | ||| | || || | | || || ||||||| ||||||||||| ||||| ||||| ||||| |||||||| || |||||||||||||| || || | || || || ||||||||||| || ||||||||
acaggcgttgcacctgatgctttgttttcttttacatcaactatatgtgacagcatcattcagaactctgttttgttaatctcaatgtcttattttgcagAGCGAATGCGCAACAACCGAAGCTGTTTGTGGGAATGATTCTGATTCTCATCTTTGCGGAAGCGCTTGCACTGTATGGTCTCATTGTTGGTATCATCCTC
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT1G75630.2 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------------------------------------------------------------------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctccattgattggtt----tgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| || ||| | | | | | | ||| | || || | ||| || ||||||| ||||||||||| ||||| ||||| ||||| |||||||| || |||||||||||||| || || | || || || ||||||||||| || ||||||||
gtaacgttgtttgatattagatttggtgttggttaagaactgtctggattgaatctttgaagcagattaggataaattaccagtagaattcaacaggcgttgcacctgatgctttgttttcttttacatcaactatatgtgacagcatcattcagaactctgttttgttaatctcaatgtcttattttgcagAGCGAATGCGCAACAACCGAAGCTGTTTGTGGGAATGATTCTGATTCTCATCTTTGCGGAAGCGCTTGCACTGTATGGTCTCATTGTTGGTATCATCCTC
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT1G19910.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------gtaagttcgatcgatcaaaagccatctttt------tcttcgatatctccattgattg-gtttgtttttct-ttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
||||||| | | || | |||| | || | | | | | | | || ||||||| | |||||| |||||||| || ||||| ||| | ||||| |||||||| || |||||||||||||| || || | || || |||||||||||||| || ||||||||
atagtcgcagctcctgatattgttgtaagttt--ttgtatggaactcgagttttgaaaggtgttatgtgtttgtaattctggtgtgtgtttttgtgttgcagAGCGAATGCACAACAACCTAAGTTGTTTGTGGGAATGATTCTGATTCTCATCTTTGCTGAAGCACTTGCCCTGTACGGTCTCATTGTTGGTATCATCCTC
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv03s0038g00790.t01 (Vitis vinifera), 3'ss of exon 2
------------------------gtaagttcgatcgatcaaaagccatctttttcttcg-atatct--ccattgattggtt---tgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
|||||| | | | | | | ||| || | | || ||| ||| | || ||| |||||||||| ||||||||||| || || ||||||||||| ||||||||||||||||||||||| || || |||| |||||||| || ||||| || || ||| ||
gactgtactttggacgactttaggataagttgctttggctgaggacaaattctttgttagtaggactaatcataatttgaatctatgatttgttttgcagGGCTAATGCGCAGCAGCCTAAACTTTTTGTTGGTATGATCCTCATTCTCATCTTTGCTGAAGCACTGGCCCTATACGGCCTTATTGTTGGCATTATCTTG
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv18s0001g13630.t01 (Vitis vinifera), 3'ss of exon 2
------------------------gtaagttcg-atcgatcaaaagccatctttttcttcga----tatctccattgattggtttgtttttc--tttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
| || ||| || || | || | |||| | | ||| | ||| || ||||| || ||||||| || ||||| ||||| || |||||||| ||||||||||||||||||||||||||||| || ||| | || || || || || ||||| || ||||||||
tttcatattaggatttctgcctttgcctttttacatctattcaattctatttatttcctttaagagtatgttt-ttgtctgaattgttgttatatttgcagAGCCAATGCTCAGCAGCCAAAGCTTTTCGTTGGAATGATCCTCATTCTCATCTTTGCTGAAGCTCTTGCCCTGTATGGACTTATTGTTGGCATCATCCTA
upper sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------------------------------------------gtaagttcgatcgat-caaaagccatctttttcttcgat---atctccattgatt---ggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
|| | || ||| | | || || | ||| || || | | | || || | |||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || || |||||||| ||||| ||||||| || || ||||| ||||| |||
gtacttgacaaagccttgcaatgtggcgatgtaccaaaatacgttttgaagttggagtcaatagtctgccaatctggattcaattcgtagaggctttacgttcatgcacgtgatatctgaggatgctgagttgatgccatttgttgatcatgtccttgttaacttggaggatggggttttgtgcagGGCCAATGCGCAACAGCCCAAGCTGTTTGTAGGAATGATCCTGATTCTGATTTTCGCCGAGGCGCTGGCTTTATACGGACTTATCGTGGGTATCATTCTGMapped 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|169036531|gb|FE444115.1|FE444115EST: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
EST:
gi|169051425|gb|FE457697.1|FE457697EST: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
EST:
gi|169051424|gb|FE457696.1|FE457696EST: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
EST:
gi|70669212|gb|DN837789.1|DN837789EST: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
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:
91TGTTCGATGGCTACGCTCATCTATCGTCCGGGCTGGCTTGCGGCCTCGCGGGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaaagccatctttttcttcgatatctccattgattggtttgtttttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG
cattgat putative branch site (score: 91)
tttgtttttctttgc putative PPT
tttgttttt TA-rich tract