Sequence
atgc intronic sequence ATGC exonic sequence...attagttgtttgtgagttgaagcataattttgcatattcatattctgttattagctttttcattgtgggcttagtttgttatcgggttcacttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------attagttgtttgtgagttgaagcataattttgcatattcatattctgttattagctttttcattgtgggcttagtttgttatcgggttcacttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
|||| | | ||| | |||| ||| || | ||||| || |||||| | || ||| |||||| || || |||| || |||| |||||||||||||||||||||||| || ||||||||||| ||||| || ||||||||||| ||||||||||||||||||||||||||||||||||| |||||
gtaaactgagcaaaaataccctgagttcttctattatagtgaaagcattattggcttgcaatctgaactatagttctacatatgcac--tctgttgtcag---------tgtaggcttaattgttt----ggttaacatattacagGGAACATGCACCATCCATTATTTTCATGGATGAAATAGACTCCATTGGATCTGCTAGGATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTCCAGCGA
upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 5
attagttgtttgtgagttgaagcataattttgcatattcatattctgtta---ttagctttttcattgtgggcttagtttgttatcg-ggttcacttatt------gcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
|||| ||| | ||| ||| || || || | | | || | |||| | | | | ||||| || ||||| | |||||||||||| ||||| ||||| || ||||||||||||||| ||| ||||||||| | ||||| ||||||| |||||||||||| ||||| || ||||||
----------aactttttgattcattaattttcatgtttatgttatttggagccttgcctaaccattattatatatgaatattatcatggaacacttgtcttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT
upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 5
attagttgtttgtgagttgaagcataattttgcatattcatattctgttattagctttttcattgtgggcttagtttgttatcg-ggttcacttattg------cagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
|| || | | |||| ||| | ||| ||| | |||| | | | || | |||| | | | | |||| || ||||| | |||||||||||| ||||| ||||| || ||||| ||||||||| ||| ||||||||| | ||||| ||||||| |||||| ||||| ||||| || ||||||
-ttgcttaacttt---ttgattcattaattttcatgt---tatttggagacttgcctaaccattattatatatgaatattattatggaacacttgtcttcttcccagGGAACATGCTCCATCAATTATCTTCATGGACGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAATGGTGATAGTGAGGTACAGCGT
upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 5
attagttgtttgtgagttgaagcataattttgcatattcat-attctgttattagctttttcattgtgggcttagtttgtta-----tcgggttcacttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
|| | | | | | || ||| ||| ||||| | ||| | ||| ||| | ||||| || || || || | | || |||||| ||||||||||| || || || ||||||||||| || |||||| |||||| | ||||| ||||| | ||| || ||||||||||| || || |
----gtaatgagcaaagtata-caccattaatcatcttcattgtgctgaaaaatacttattc-cagctagcttacctttctagtacctctggcttatggttttcagGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATCGGGTCTGCTCGTATGGAATCTGGTAGTGGAAATGGTGACAGTGAGGTGCAAAGG
upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 5
-------attagttgtttgtgagttg--aagcataattttgcatattcatattctgttattagctttttcattgtgggcttagtttgttatcgggttcacttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
||| ||| || | || | || | | | || || | || ||| || || |||||| | ||| || | || |||||| ||||||||||| || || || ||||||||||| || ||| || |||||| | ||||| ||||||| ||| || ||||||||||| || || ||
cacagtgccaagtctcatgtaaggagcaaattacaaataggtgagatgattcgttgaaaatactctttcca--gttggctta------caccgg-tttatggttttcagGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATTGGGTCTGCTCGTATGGAATCTGGAAGTGGAAATGGTGACAGTGAGGTGCAACGG
upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
attagttgtttgtgagttgaagcataattttgcatattcatattctgttattagctttttcattgtgggcttag--tttgttatcgggttcac--ttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
|| | | || |||| | | | |||| | |||| | ||| | ||| ||| | | | | || || |||||| ||||||||||| || || ||||||||||| |||||| ||| ||||||||| | ||||| || |||| |||||| ||||| |||||||| |||||
----gtagagcccatcatcaacaataacaaaaaggaaaaaaaaaatgttgctttctttgttgctgtttgtttaaactttactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG
upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------------------------------------------------------------------------attagttgtttgtgagttgaagcataattttgcatattcatattctgttattagctt---tttcattgtgggctta--gtttgttatcgggttcacttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
|| |||||| |||| | | | || | | ||| |||| | | | ||| || || |||| || | || || | | | ||||| |||||| ||||| ||||| || || || ||||||||||||||| ||| ||||||||| ||||||| ||||||||||| || ||||| |||||||| |||||
gtttgtttaatatctttagtggaaaccatgacttgtgatacacctagaggatttatttttcactcataagataatattttatatgttacctctcctgggtaattgttta-gagtcacatttttttcctgggttattgaattttgttttaaatctcccttttatcttgtccttatggtctcttctctgctgc-tttattacagGGAGCATGCTCCATCAATCATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGAATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGA
upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 5
lower sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 5
attagttgtttgtgagttgaagcataattttgcatattcatattctgttattagctttttcattgtgg-gcttagtttgttatcgggttcacttattgc----agGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
| |||| || | || | | | | | | ||| | | || ||||| | ||| || | ||||||||||||||||| || || || |||||||||||||| ||| ||||| ||| | |||||||||| | |||||| || || ||||||||||||||
-----taagatgtgtttttgattgccatcaacggaacttgtctctacctggaaacttcatgtcaagaacgtataagatgttaacaagttatttttgtatggttagGGAACATGCACCATCAATCATCTTCATGGATGAAATTGATAGTATTGGATCAGCTCGTGTGGAGTCTGGGAATGGCAATGGAGATAGTGAAGTTCAGCGGMapped 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|67018679|gb|CO447428.1|CO447428EST: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAG GGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
genomic: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
EST:
gi|6564061|gb|AW231683.1|AW231683EST: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAG GGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
genomic: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
EST:
gi|60352424|gb|DN219397.1|DN219397EST: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAG GGAACATGCACCATC
genomic: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATC
EST:
gi|60351658|gb|DN218631.1|DN218631EST: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAG GGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
genomic: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
EST:
gi|211122652|gb|FL433068.1|FL433068EST: GGAACTCTTTGTTATGGCCAG GGWACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
genomic: GGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
EST:
gi|5847445|gb|AW000524.1|AW000524EST: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAG GGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
genomic: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
EST:
gi|20301129|gb|BQ164072.1|BQ164072EST: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAG GGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
genomic: TATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATC
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 4 RNA-Seq libraries.
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
300ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTGAGTTGGTTCAGAAGTATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
256ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTGAGTTGGTTCAGAAGTATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
203ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTGAGTTGGTTCAGAAGTATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
279ACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTGAGTTGGTTCAGAAGTATATTGGTGAGGGCTCCCGGATGGTTAGGGAACTCTTTGTTATGGCCAGgtaggctgag ... cttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttattagctttttcattgtgggcttagtttgttatcgggttcacttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
ttcactt CT-rich tract
tttttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attagttgtttgtgagttgaagcataattttgcatattcatattctgttattagctttttcattgtgggcttagtttgttatcgggttcacttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT
- - - tgtttgt
- - - - - - - - -tgaagca
- - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - ttcatat