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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgatgttaagttgccgctcttctcatttgccctttttggctactgttccttgttttctggtaactaatcttggttaaatattatctacaattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTCTACGTCTACTGGATATGCCCTTTTGTTGGCGCTGTTCTTGCTGCCTGGG

Basic information

species Oryza sativa
transcript LOC_Os01g08660.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G113470_T01 (Zea mays), 3'ss of exon 2
tctgatgttaagttgccgctcttctc----atttgccct--ttttggctactgttccttgttttctggtaactaatcttggttaaatattatctacaattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTCTACGTCTACTGGATATGCCCTTTTGTTGGCGCTGTTCTTGCTGCCTGGG
   | | | |  |  ||||| |   |    |   ||  |  |  |  ||    |||||| ||  || |||| | || ||  ||    | |    |  |    | |||| ||||||||||||||||| |||||| | |||||||||||||||||  | || || |||||||||||||| ||| |||| ||  | |||||||  ||| 
--cgttttcagttaaccgctttgtacgaaaacaagcattaatcctatcttgatttcctttttaacttgtaatttatgttttttggtcaattgtcatga----atagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA

upper sequence: LOC_Os01g08660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G060922_T01 (Zea mays), 3'ss of exon 2
tctgatgttaagttgccgctcttctcatttgcccttttt-----ggctactgttccttgttttctggtaact-----aatcttggttaaatattatctacaattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTCTACGTCTACTGGATATGCCCTTTTGTTGGCGCTGTTCTTGCTGCCTGGG
 |   |  |  |||||   | |||   || || || |||     |  ||  | | ||  ||||||| |  |         |||| | ||||||||||||||        ||| ||||||||||||||||| ||||| ||||| || || |||||||| ||||| || ||||||||||| || ||  |||| ||  |||||||||| ||| 
-ccatttctctgttgcta-ttttcagtttagcgctctttactaagaataaagattctacttttctgttttccttaacggccttgatgaaatattatctaca--------gGCATTTGGCTGGGCATATGTTAACAACCGCCATAATACGTGGGAGCAGTTCTATGTGTACTGGATATGTCCCTTCATTGGTGCCATTCTTGCTGCGTGGA

upper sequence: LOC_Os01g08660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G26720.1 (Glycine max), 3'ss of exon 2
tctgatgttaagttgccgctcttc--tcatttgccctttttggctactgttccttgttttctggtaactaatcttggttaaatattatctacaattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTCTACGTCTACTGGATATGCCCTTTTGTTGGCGCTGTTCTTGCTGCCTGGG
 ||||   |   |||    |  ||  | |  |    | ||    || ||||    ||  | |    |  |    |   | |||  |   ||  |||   ||||| ||||| ||||||||  |  | ||  | |||||||||||||| |||||||| || |||||||| ||||| ||  |||| ||  | || ||||| ||| 
-ctgaccattttttgtttttggtcagtaacataagatattaatgtaatgttgtgagtcatatatgcatgatgaataactcaatgattggtattatttt-cagGCATTTGGTTGGGCATACTTTGAAAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCTTTGGAGCAATACTGGCTGCATGGC

upper sequence: LOC_Os01g08660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G28430.1 (Glycine max), 3'ss of exon 2
-----tctgatgttaagttgccgctcttctcatttgccctttttggctactgttccttgtttt-ctggtaactaatcttggttaaatattatctacaattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTCTACGTCTACTGGATATGCCCTTTTGTTGGCGCTGTTCTTGCTGCCTGGG
       || | || | |   |    ||    ||     |  || | | ||   ||| |   | |   | | |||   || |    |||| ||       |  ||||| ||||||||||||||  | |||||  | |||||||||||||| |||||||| || |||||||| || || ||    || ||  |  | ||||| ||| 
cttctcttgtttttgaatcttctgattttaatttcagtttgattaggttctagacctagagatgccaatgaataactgtgatcggttattgtc------cctgcagGCTTTTGGCTGGGCATACTTAAACAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGTCCCTTCACCGGAGCAATATTGGCTGCTTGGC

upper sequence: LOC_Os01g08660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G04800.1 (Glycine max), 3'ss of exon 2
tctgatgtt----aagttgccgctcttctcatttgccctttttggctactgttccttgttttctggtaactaatcttggttaaatattatctacaattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTCTACGTCTACTGGATATGCCCTTTTGTTGGCGCTGTTCTTGCTGCCTGGG
||| |||||    ||  | | | | ||   ||  |     || || |   |         |||   | | ||| ||| || |  | ||||   |    |  ||||| ||||||||||||||  | |||||  | |||||||||||||| |||||||| || |||||||| ||||| || |  || ||  |  | ||||| ||| 
tctcatgtttttgaatcttctgatgttaatatcagtttgattagggtctagacttagagattccaatgaataa-ctttgtgatgtgttattgtc---cctgcagGCTTTTGGCTGGGCATACATAAACAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCGCCGGAGCAATATTGGCTGCTTGGC

upper sequence: LOC_Os01g08660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G07680.1 (Glycine max), 3'ss of exon 2
-tctgatgttaagttgccgctcttctcatttgccctttttggctactgttccttgttttctggtaactaatcttggttaaatattatctacaattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTCTACGTCTACTGGATATGCCCTTTTGTTGGCGCTGTTCTTGCTGCCTGGG
 | |      |  ||     | || | |  |    | ||    || ||||    ||  | |    |  |    |   | |||  |   ||  |||   ||||| ||||| ||||||||  |  | ||  | |||||||||||||| |||||||| || |||||||| ||||| ||  |||| ||  | || ||||| ||| 
ctttctgaccatttttttctttttgtaacataagatgttaatgtaatgttgtgagtcatatatgcataatgaataactcaatgattggtattatttt-cagGCATTTGGTTGGGCATACTTTGAAAACTGGCACAACACATGGGACCAATTCTATGTATACTGGATTTGCCCCTTCTTTGGAGCAATACTAGCTGCATGGC

upper sequence: LOC_Os01g08660.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0007g07680.t01 (Vitis vinifera), 3'ss of exon 2
---tctgatgttaagttgccgctcttctcatttgccctttttggctactgttccttgttttctggtaactaatcttggttaaatattatctacaattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTCTACGTCTACTGGATATGCCCTTTTGTTGGCGCTGTTCTTGCTGCCTGGG
   |  |   ||| | |   |   |  |  |  ||  ||  | ||| |  || |   | ||       |||||  |  ||| || |||| |     ||  ||||| ||||| ||||||||| | |||||| | || ||||||||||| || || ||||| |||||||| ||||| ||  | || ||  |  | ||||| ||||
tgttggggcattacgat-ttgaaatgatggtcagcatttccttgctcccttttccattatttaaaagcctaattatatttatat-ttattt-tgtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTGTACGTTTACTGGATCTGCCCCTTCATAGGGGCAATATTGGCTGCATGGG

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|88852698|gb|CI008891.1|CI008891
EST:     TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|13896286|gb|AU182622.1|AU182622
EST:     TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|88832544|gb|CI008140.1|CI008140
EST:     TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|8527635|gb|AU092450.1|AU092450
EST:     CCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCATATNTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: CCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|88220711|gb|CI220271.1|CI220271
EST:     CCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: CCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|86595472|gb|CI264569.1|CI264569
EST:     TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|58676508|gb|CK065195.1|CK065195
EST:     TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|89179702|gb|CI043981.1|CI043981
EST:     TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|87022976|gb|CI279993.1|CI279993
EST:     TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|29675794|gb|CB672069.1|CB672069
EST:     TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|88845691|gb|CI008688.1|CI008688
EST:     TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTTCCAAT                         GCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|86843358|gb|CI341439.1|CI341439
EST:     CTCACCGGCGCGGCCTACACTGGCCCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: CTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|9788894|gb|BE530904.1|BE530904
EST:     ACACTGG-CCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: ACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|87007022|gb|CI275330.1|CI275330
EST:     TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCAAATGTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|88850523|gb|CI093204.1|CI093204
EST:     TCGTCCTTACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|3762326|gb|C99574.1|C99574
EST:     TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCATATGTGNACAATCGCCACAACACATGGGNGCAATTC
genomic: TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
EST: gi|86822571|gb|CI358070.1|CI358070
EST:     AACCCTGCCAAT                         GCGTTTGGGCTGGGCATATTTGAACAATCGCCACAACACATGGGAGCAATT
genomic: AACCCTGCCAATgtgagatttc ... aattccacagGCGTTT-GGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATT
EST: gi|88836553|gb|CI010809.1|CI010809
EST:     TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAAT                         GCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC
genomic: TCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTC

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: 74 (upstream exon), 48 (downstream exon)
Score: 9

CCGTAATCCCATCGTCAAGACCTGGATGCTCTCCATCTCCACCGTTTGCCTCGTCCTCACCGGCGCTGCCTACACTGGCCCATCCATGAACCCTGCCAATgtgagatttc ... aattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTCTACGTCTACTGGATATGCCCTTTTGTTGGCGCTGTTCTTGCTGCCTGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttccttgttttctggtaactaatcttggttaaatattatctacaattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTCTACGTCTACTGGATATGCCCTTTTGTTGGCGCTGTTCTTGCTGCCTGGG
                  aactaat  putative branch site (score: 9)
                              ttaaatattatctaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgatgttaagttgccgctcttctcatttgccctttttggctactgttccttgttttctggtaactaatcttggttaaatattatctacaattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTCTACGTCTACTGGATATGCCCTTTTGTTGGCGCTGTTCTTGCTGCCTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
-ctgatgt
- - - - - - - gccgctc
- - - - - - - - - - - - -catttgc