Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagcttaccctagatctccatcgcgttctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttctcgcaattcttccag

Basic information

species Selaginella moellendorffii
transcript EFJ24104
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os12g37360.1 (Oryza sativa), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagcttaccctagatctccatcgcgttctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttc--tcgcaattcttccag-
| ||||  |||| |||||||||||||||||||||||||| |||||||| || |||||||| || || || || ||||| |||||||||||||||||||||||   | |   | |  || |  |   | |   |    ||  |  | ||  ||   ||   | |  || |||  | || |    ||||  | |   |   |   | 
GCTGGCGTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACGCTCCTCCACATGCTCAAGGACGAGgt---tcgccacgaagtttctttccttttgtttta-attgagcagtcgattcatctgt-tggttgttaggtgatctgatgcggtttcgattgggttggattatgc

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os01g15010.1 (Oryza sativa), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagcttaccctagatctccatcgcgttctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttctcgcaattcttccag
| ||||| |||| |||||||||||||||||||||||||| |||||||| || |||||||| || || || || || || |||||||||||||||||||||||  || |   || | |    | |    || |||| | | ||   | |  |   |||       || || ||| |  |    |||    |||          
GCTGGCCTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaggtcgc--ccggatcgatcga----tcgatcgagatttgta-ctgatttggttgg------ttctgatttgtgttgggatttgggtgcag---------

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os01g23620.1 (Oryza sativa), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagcttaccctagatctccatcgcgttct--gaggccgcctctcttgcgcgctcttttggttttttgtt--ttcttttctcgcaattcttccag-----------------------------
| | ||  |||| |||||||||||||||||||||||||| |||||||| || |||||||| || || || || || || |||||||||||||||||||||||       | ||  |||  ||  ||||||  || | | |       || |   |||  | || ||  ||    ||| |||   |||  ||   |  |  ||                                 
GCTCGCGTCGCTGGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTCAAGGACGAGgtaccctcctacc--cttcgcccggatctctctcccctcccccacaaccccagatctgacccgatccatttccctttcgttggatctgatccgtctgtgtttgtgcgtgcgtgcgtgcgtgggcggatggtgcag

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os06g12090.1 (Oryza sativa), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagct--taccctagatctccatcgcgttctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttctcgcaattcttccag-
| ||||  || |||||||||||||||||||||||||||| |||||||| || |||||||| || || ||||| || ||  || ||||||||    | |||||    || | ||| |   |  ||||     ||   |       | |||   | |             ||  ||||  | ||  ||||     | ||    |   
GCTGGCGTCGATCGGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAAACCACCCTCTTCTACATGCTCTCACAAGAGgtata-ggctcccatcggatggcctaatcaaccgaagaa----aatgccaaattttaaatttttaaacttaattttgagattgattttaagatattttcaacgta

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G038356_T01 (Zea mays), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtg---gtttccagcttaccctagatctccatcgcgttctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttctcgcaattcttccag
| ||||| | ||||| ||||||||||||||||||||||| |||||||| || |||||||| || || || || ||||| |||||||||||||||||||||||  |     ||  || |  | |    | | |||      | ||    | || || || |      ||  |   |  |||||| |  |  | |||          
GCTGGCCTCCCTCGGCCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTTGGCCTCGACAACGCCGGCAAGACCACGCTGCTCCACATGCTCAAGGACGAGgtacgccaccgtcccccgtctgcttccggtatcc----tatcctagatctgcttccctgggcttgcctgatccgtgcttgttt-cgatcgttgcag---------

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G181536_T01 (Zea mays), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttc-cagcttaccctagatctccatcgcgttctgaggccgcctc--tcttgcgcgctcttttggttttt----------tgttttcttttctcgcaattcttccag----
  |  ||  ||   ||||||||||||||||||||||||| |||||||| || |||||||| || || || || ||||| |||||||||||||||||||||||      | |  |  | |    | | |  | | | | | | |  |  |  |   ||| ||| ||      || |  |           |   |  | | |||   || | | |     
TGTCTCCCTGCGGCGGCTGTGGCAGAAGGAGGCCAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACGCTGCTCCACATGCTCAAGGACGAGgtacacattctggcgccctggttttgcttgctaccacatgcagttgatgatttcttctcgcgtgccggccgggatagtgaacaacggtcgccctgctgtgtcgtcgttgtgctatgcag

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G086636_T03 (Zea mays), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagt---ggtttccagcttac---------cctagatct--ccat-cgcgttctgaggccgcctctcttgcgcgctcttttggttttttg-ttttcttttctcgcaattcttccag
| ||||| | ||||| ||||||||||||||||| ||||| |||||||| || |||||||| || || || || ||||| |||||||||||||||||||||||  ||    ||  || || | |         |||||||||  ||   | || |  ||  | | |  | |   ||   | ||||  ||| || |    | || || | ||   | |||
GCTGGCCTCCCTCGGCCTGTGGCAGAAGGAGGCGAAGATCCTCTTCCTCGGCCTCGACAACGCCGGCAAGACCACGCTGCTCCACATGCTCAAGGACGAGgttcgtcgccgtcccccgcctgcttcccgtatcctagatctgaccgcacccgattggatcctgtccatttctggcttccgtttgcctttctgatccgttcttgtctcgatcgctgcag

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G122666_T01 (Zea mays), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagt--ggtttccagcttaccctagatctccat-cgcgttctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttctcgcaattcttccag
| ||||  |||| |||||||||||||||||||| ||||| |||||||| || |||||||| || || || || || || ||||||||||| |||||||||||          |||  | | | |    | ||| | ||  |||          |   ||   |        | ||  |  | |  ||   | |   |  |  |||
GCTGGCATCGCTTGGGCTGTGGCAGAAGGAGGCTAAGATCCTCTTCCTTGGCCTCGACAACGCCGGCAAGACCACCCTCCTCCACATGCTGAAGGACGAGgtcctctctacctccgacatccgccccttttccttgcgaattccagtcttatatgctttcgacttaacggggattcctgatctggttcgattgggttcatcgcag

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA07G37070.1 (Glycine max), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagcttaccctagatctccatcgcgttctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttctcgcaattcttccag
  | ||  | ||||| || |||||||| || ||||| ||||||||||| |||||||| ||||| ||||| || || ||||| ||||||||||| |||||||||||     ||   |||| | |  |  |  |||   |    |     | | | ||        | ||  |||||| ||   |||| |||      || |||
TCTAGCTTCCCTCGGTCTCTGGCAGAAAGAAGCCAAAATTCTCTTCCTTGGTCTCGATAATGCAGGGAAGACCACACTTCTTCACATGCTCAAAGACGAGgtgaggttcctctcccttaacatcaaaat--atcaaatc---aaatacctttttttat---tattattaatttttttttcatttttttcgatgcaattgcag

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA17G03540.1 (Glycine max), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagcttaccctagatctccatcgcgttctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttctcgcaattcttccag-----------
  | ||  | ||||| || |||||||| || ||||| ||||||||||| |||||||| ||||| ||||| || || || || ||||||||||| |||||||||||     ||   |||| | |  |  |  |||   |       ||   | | ||      | ||||  |||| | | ||      |   |||| || |             
TCTAGCTTCCCTCGGTCTCTGGCAGAAAGAAGCCAAAATTCTCTTCCTCGGTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcctctcccttatcatcaaaat--atcaaatcaaatacccttttttatttttattttttttatttttatctattaaaaagttttaattttttcgatgcaattgcag

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA09G04290.1 (Glycine max), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagcttaccctagatctccatcgcgttctgaggccgcctctcttgcgcgctcttttggttttttgt-------tttcttttctcgcaattc--ttccag
  | ||  | ||||| || |||||||| || ||||| ||||||||||| |||||||| ||||| || ||||| || || || ||||||||||| |||||||| |    |||||  ||  | ||    || | ||   || |    |    | |         |  |||  ||    |         ||   || | | ||||   || |||
TCTCGCTTCCCTCGGTCTCTGGCAGAAAGAAGCCAAAATTCTCTTCCTTGGTCTCGATAATGCCGGCAAAACCACCCTCCTTCACATGCTCAAAGACGAGgttacc--tttccctctctctcttacccttc-tcattttttttttcaatttttgaaaaaaattgattttcttaaaagaaaaaaaaattgaatttttgaaatttggttgcag

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA15G15330.1 (Glycine max), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagcttaccctagatctccatcgcgtt-ctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttctcgcaattc--ttccag
  | ||  | ||||| || |||||||| || ||||| ||||||||||| |||||||| ||||| || ||||| || || || ||||||||||| |||||||| |      |||  ||   |    | |    ||   || ||    ||   | |            |  |          ||   || | | ||||   || |||
TCTCGCTTCCCTCGGTCTCTGGCAGAAAGAAGCCAAAATTCTCTTCCTTGGTCTCGATAATGCCGGCAAAACCACCCTCCTTCACATGCTCAAAGACGAGgttaccttcctccctctcctctcttacccttctcatttttcttcttccaatttttgaaaaaaaaaataagaaaaaaaaaattgaatttttgaaatttggttgcag

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA19G41670.1 (Glycine max), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagcttaccctagatctccatcgcgttctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttctcgcaattcttccag
  | ||  |||||||||||||||||||||||||||||||  | ||| | || ||||| || || || ||||| ||  | || ||||||||||| || |||||   || |||||   ||    |   | |||       | |    ||   | | ||      | || |     || |||||                     
TCTAGCGTCGCTCGGGCTGTGGCAGAAGGAGGCCAAGATCTTATTCTTGGGCCTCGATAACGCTGGCAAAACTACCTTGCTTCACATGCTCAAAGATGAGgttt-tgttttccttttttttttttgtttccccaatcgttta---ccttttttttttattattattataagagttggttttgcag-----------------

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA10G28910.1 (Glycine max), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagctta-ccctagatctccatcgcgtt-ctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttctcgcaattcttccag-
  ||||  |||| ||| ||||||||||||||||||||||  | ||| |||||||||| ||||| || || || ||  | || ||||||||||| ||||||||      |||||   | | ||||  ||| |  |    || ||| |   |    ||||      |  || |  |  || | | |  ||     | |  | | || 
TCTGGCATCGCTTGGGTTGTGGCAGAAGGAGGCCAAGATCTTATTCTTAGGTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttcccttttccgcttaagccctgaatcgctttaaatttactgggaatgttattctt-----ttagttagaatccttttgtacaatttaaatattattacgaga

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA20G38360.1 (Glycine max), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagcttaccctagatctccatcgcgttctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttctcgcaattcttccag
  ||||  |||| ||  ||||||||||||||||||||||  | ||| |||||||||| ||||| || || || ||  | || ||||||||||| ||||||||      || ||| | |   |    | |   ||   | ||    |     | |||  || ||   | | |||    ||| ||         |||| |  | 
TCTGGCATCGCTTGGATTGTGGCAGAAGGAGGCCAAGATCTTATTCTTAGGTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttccctttcccatccttttccgcttatttctctgctccttcttcacaaacgcttaagccctgaatcgatttaa-atttactgggaatcttattcgttta-

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv07s0005g01330.t01 (Vitis vinifera), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagt---ggtttcc---agcttaccctagatctccatcgcgttctgaggccgcctctcttgc------gcgctcttttggttttttgttttcttttctcgcaattcttccag
  | ||| | |||||  |||||||||| |||||||||||  | || ||||||||||| ||||| || ||||| ||| | || |||||| | ||||| |||||| ||   | ||  |   || || || |   | | |   | |     |       | | |||       |   ||| |     | ||| ||  | ||    |  || || |||
TCTCGCCTCCCTCGGCTTGTGGCAGAAAGAGGCCAAGATCTTGTTTCTAGGTCTCGATAATGCCGGAAAAACGACGTTGCTTCACATGTTGAAGGATGAGgtgtgttttgattctctacagttttccttttcttttcccggggaagcaaatggagttttgttgttttattgttttctgtaccaatcttgattgttctttggactgtttttacag

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S10_357V6.1 (Physcomitrella patens), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagcttaccctagatctccatcg--cgttctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttctcgcaattcttccag-
  | || |   | ||||||||||||||||||||||| || || || || |||||||||||||| || || || || ||||| |||||||||||||| ||||| ||   | ||     |    |   ||    | |  |  | | |   |||   |  |  |||  |       |||| |  |           ||    |||   
TCTTGCGAGCATAGGGCTGTGGCAGAAGGAGGCCAAAATCCTGTTTCTGGGTCTCGACAATGCTGGCAAGACTACTCTTCTGCACATGCTCAAGGATGAGgttag-actctcttttctgttttgattcctgcttggtcaatttcaattcgcggttgata-gcgtacc---aaattttcgcctctagaatcgataacgtatccgtt

upper sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S44_58V6.1 (Physcomitrella patens), 5'ss of exon 1
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggttt-ccagcttaccctagatctccatcgcgttctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttctcgcaattcttccag
  | || |   | ||  ||||||||||||||||||| ||  | ||||| ||||| |||||||| ||||| || || ||||| |||||||||||||| |||||       || |||| || |      | |   |    || |    | |  | |     ||   |  | |   | | | ||||| |  ||     |  |    
TCTTGCGAGCATAGGTTTGTGGCAGAAGGAGGCCAAAATCTTGTTCCTGGGTCTTGACAATGCCGGGAAGACGACACTTCTGCACATGCTCAAGGATGAGgtcctccccttgccagatttcttctccttttttttcttttttcccacggtttgtgcctggctgccgctagaaatgtcggtttctgtcttcatggcttctg---

Mapped 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|169116156|gb|FE517935.1|FE517935
EST:     GTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAG                         AGATTGGTACAGCACCAGCCCACCCAGTATCCAACATCCGAGGAGCTAAGC
genomic: GTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtt ... attcttccagAGATTGGTACAGCACCAGCCCACCCAGTATCCAACATCCGAGGAGCTAAGC
EST: gi|70670465|gb|DN839042.1|DN839042
EST:     GTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAG                         AGATTGGTACAGCACCAGCCCACCCAGTATCCAACATCCGAGGAGCTAAGC
genomic: GTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtt ... attcttccagAGATTGGTACAGCACCAGCCCACCCAGTATCCAACATCCGAGGAGCTAAGC

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: 35 (upstream exon), 35 (downstream exon)
Score: 38

GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtt ... attcttccagAGATTGGTACAGCACCAGCCCACCCAGTATCCAACATCCGAGGAGCTAAGCATCAACAAGATCAAATTCAAGGCCTTCGATCTGGGGGGTCACCAGATCG




<











<


<