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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcccgaccgattttttgttgttttgttcgatctggtagtgttagtggatgttgattgattagtttgctcgcttaatccgaattgtagggtagg...

Basic information

species Oryza sativa
transcript LOC_Os05g41110.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g41110.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G044137_T02 (Zea mays), 5'ss of exon 2
AGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcccgaccgattttttgttgttttgttcgatctggtagtgttagtggatgttgattga--ttagtttgctcgcttaatccgaattgtagggtagg
||||| || | ||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||||||| ||      |||| |   |  |||  |  ||   |     |  | ||  | || |||  ||     |   ||       || ||||| |   | 
AGCACAGAGAGCATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTGGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgattccatttctttttctaa-gcgttgccctttcctttccctctgataga-atcgaatgacattgagccgtatgcccgtatggatttgtacgagtga

upper sequence: LOC_Os05g41110.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv13s0064g00850.t01 (Vitis vinifera), 5'ss of exon 2
AGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcccgaccgattttttgttg-----------ttttgttcgatctggtagtgttagtggatgttgattgattagtttgctcgcttaatcc---gaattgtagggtagg-----
|     || |||||||||||||||||    || ||||||||||||||||||||||||||||||||||||||||| |||||||  ||  | | |||||||||| | | |    |    |||  | ||            | || |    ||| | | | || |||  | | |  |   |  ||  |    | | |     ||| |    | |        
ACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgt-ttgttatacatttttttcatattaagagctacagatcttttctcttcttgcatttttggtgtgtttggggtttgtgattatcggattaagttttgggaaatacttgatgatggcag

upper sequence: LOC_Os05g41110.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EDP06387 (Chlamydomonas reinhardtii), 5'ss of exon 2
AGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgta--------------tcgatcccgaccgattttttgttgttttgttcg-atctggtagtgttagtgga-tgttgattgattagt-ttgctcgct-taatccgaattgtagggtagg--------------------------------------------
| |  ||| |||||||||  |   |||  ||||||||||||||| ||||||||||| || ||||||||||||  ||| ||||| ||||||     ||||||||               |||  ||  |||| |  |  ||  |     || | |   |     | |||   |||     | | ||    || ||||    ||   |    |     |                                             
ACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGGGCAAGGgtaagtttgcgctcgcgccgacgcccgccgactggtgcttcctcaacccgcaccccctgccccttgtgccctgtgtggggctcagcaccgcacgctgccttctccaccagaaaactgcacatctatctcaccaactttgtctcctcttcttgcccaccgcag

upper sequence: LOC_Os05g41110.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ14031 (Selaginella moellendorffii), 5'ss of exon 1
AGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcccgaccgattttttgttgttttgttcgatctggtagtgttagtggatgttgattgattagtttgctcgcttaatccgaattgtagggtagg
| |  ||| | |||||||||||   ||  |||||||||||||||||||||||||||||| ||||||||||| || |||||  |||||||||     || ||| |  |  ||  |   ||| ||  | ||  | | ||||   | | |  | ||| ||   |                                       
ACCCAGGAGAGCATCAACAACAGATTGGCGCTGGTGATGAAGAGCGGCAAGTACACGCTGGGCTACAAGACGGTGCTCAAATCGCTGCGCAGTGGAAAAGgtgtgaaatccctc---tttgtttctcttgcgattgatccattggcgc-attgggtgcgcag--------------------------------------

upper sequence: LOC_Os05g41110.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ13021 (Selaginella moellendorffii), 5'ss of exon 1
AGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtat-cgatcccgaccgattttttgttgttttgttcgatctggtagtgttagtggatgttgattgattagtttgctcgcttaatccgaattgtagggtagg
| |  ||| | |||||||||||   ||  |||||||||||||||||||||||||||||| || |||||||| || |||||  ||||||| |     || ||| |  ||   |  ||  ||| ||  | ||  | | ||||  || | |  | ||| ||   |                                       
ACCCAGGAGAGCATCAACAACAGATTGGCGCTGGTGATGAAGAGCGGCAAGTACACGCTGGGGTACAAGACGGTGCTCAAATCGCTGCGGAGTGGAAAAGgtgtgtgaaatc--cctctttgtttctcttgcgattgatccagtggcgc-attgggtgcgcag--------------------------------------

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|88208991|gb|CI208840.1|CI208840
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|30228744|gb|CB966634.1|CB966634
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|14981077|gb|BI305768.1|BI305768
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|27578251|gb|CB000946.1|CB000946
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|30228625|gb|CB966515.1|CB966515
EST:     TACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGNG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAG
genomic: TACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAG-Ggtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAG
EST: gi|87025758|gb|CI282335.1|CI282335
EST:     ACGCTCGGCTACAAGACCGTCCTCGAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: ACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|87023003|gb|CI280020.1|CI280020
EST:     CTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: CTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|58594776|gb|CF993084.1|CF993084
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCGGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|87032220|gb|CI262002.1|CI262002
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|86593179|gb|CI255641.1|CI255641
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|53553193|gb|CO435745.1|CO435745
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|29686201|gb|CB682476.1|CB682476
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|86530215|gb|CI170421.1|CI170421
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|58031073|gb|CX728616.1|CX728616
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|87011660|gb|CI281362.1|CI281362
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|86532355|gb|CI172561.1|CI172561
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|86417527|gb|CI031736.1|CI031736
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|88400326|gb|CI591016.1|CI591016
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|86599456|gb|CI251414.1|CI251414
EST:     GTACACGTTCGGCTACAAGTCCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|86533322|gb|CI173528.1|CI173528
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|55410942|gb|CV723318.1|CV723318
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|86416886|gb|CI030897.1|CI030897
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|86835219|gb|CI346694.1|CI346694
EST:     GTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|86529357|gb|CI169563.1|CI169563
EST:     ACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: ACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
EST: gi|88991955|gb|CI035093.1|CI035093
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGG                         GGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGA

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: 75 (upstream exon), 75 (downstream exon)
Score: 122

AGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcc ... ttatgtttagGGAAGCTGATTATCCTTGCAAACAACTGCCCTCCACTCAGGAAGTCTGAGATTGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCACGGACAACATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAAGACGCTGCGCAACTCCAAGGgtatcgatcccgaccgattttttgttgttttgttcgatctggtagtgttagtggatgttgattgattagtttgctcgcttaatccgaattgtagggtagg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccgacc