Sequence
atgc intronic sequence ATGC exonic sequencegtacaatcccctacatattgccgtgctttttggtgattcctcgagttatttactgaacactctacttacaagtcctttttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
-----gtacaatcccctacatattgccgtgctttttggtgattcctcgagtt--atttactgaacactctacttacaagtccttttt-----ctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
| ||| | | |||||||| | || | || |||| | | | | || |||| || | |||| || ||||||||||||||||||| |||||||||||||||||| ||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |
gttactctccatctcat-catattgcaaacatattatcatactcacacagttggaatctcacagtgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA
upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 18
---------------gtacaatcccctacatattg------ccgtgctttttgg---tgattcc-tcgagttatttactgaacactctacttacaagtccttt---ttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
| | ||| | | | | ||||| || | | |||| || | | || | |||||| || || || ||| | ||||||||||||| ||||| ||||||||||| || |||||||||| |||||||| ||||||| |||||||| ||||| ||||||||||||||||| | || |
gtgattgtttgtgcccttttgctacttacgtgtcgttccagctttgcttattagaagttattctgtcaggagagttcataaacactgtattttaaatcgttttgcttgctcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAGTGACATTGATGTTACTTTTGATGATATTGGAGCTCTTGAAA
upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 20
--------------------------------------------------------------------gtaca-atcccctacatattgccgtgctttttggtgattcctcgagttatttactgaacactctacttacaa--gtcctttttct------------cagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
| || | | | | || || || | | | || || | || ||| ||| || | || || ||| | || | ||||||||||| ||||| || || ||||| || |||||||||| |||||||| |||||||| |||||||| ||||| || |||||||||||||| | || |
gtgattgttatggagttttgctactttgattgtgggagatagtgacatgacatccagtagtttgttccgaacttactgcttggaagttattctg-ttgatagagtttaatcaatttttttcacgaatgctgtgttttgaattatccctcttatgttttttgaaatcagGATGTTGTAACAGAAAACGAGTTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAACGACATTGGTGTTACTTTCGATGATATTGGAGCTCTTGAAA
upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 19
------------------------------------------------------------------gtacaatcccc-tacatattgccgtgctttttggtgattcctcgagttatttactgaacactc-tacttacaagtcctttttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
||| | | ||| | | | | || ||| | || || | | ||| || | |||| |||||||| || || ||||||||||||||||||| ||| | | |||||||| ||||| | ||| ||||| || || ||||||||||||||||| || || |
gtaatttaatataagatgttacaaacttaaacctttttccatcatattttgtggagatattttgcattactactggtattcatctagtttctttaccttgtcattttttgaattgtgggattgtcacctgtattcttggaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCACCAACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------gtacaatcccctacatatt-gccgtgctttt--tggtgattcctcgagttatttactgaacactctacttacaa--gtcctttttct------------cagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
||| || | | | | || || | | | || |||| |||||| |||| | | | || ||| | || | ||||||||||| ||||| || || ||||| || |||||||||| |||||||| ||||||||||||||||| ||||| ||||||||||||||||| | || |
gtgattgttatggacttttgctgctttgattgtgagagatagtgacatccagtagtttgttcccaacttactgcttggaagttattctgttgatagagtttaatcgatttatttcatgaatgttgtgttctgaattatccctcttatgttttttgaaatcagGATGTTGTAACAGAAAACGAGTTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAATGACATTGGTGTTACTTTTGATGATATTGGAGCTCTTGAAA
upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 16
---------------------gtacaatcccctacatattgccgtgctttttg---gtgattcc-tcgagttatttactgaacactctacttacaagtccttt---ttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
||| | | | || ||||| || || |||| ||| | | || | |||||| || | || ||| | ||||||||||||| ||||| ||||||||||| || |||||||||| |||||||| ||||||| |||||| | ||||| ||||||||||||||||| | || |
gtgattgtttgtgcccttttgctacttacatgtgattccagctttgcttattacaagttattctgtcgggagagttcataaacactgtattctaaatcattttgcttgctcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAGTGACATCGATGTTACTTTTGATGATATTGGAGCTCTTGAAA
upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 19
gtacaatcccctacatattgccgtgctttttggtgattcctcgagttatttactgaacact--ctacttacaagtcctttt-tctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
||| || | || |||| ||| ||| ||| | ||| | ||| | | | | | | | | || | |||||||||||| |||||||||||||| ||||||| || | || || || || || | ||| || || ||| | || ||||||||| || ||||| |
--gtaattatatagaaatc-ttatgctattt--tgactcc--aaattaacttctggattttaacaattattatgctatattatttcagGATGTTGTTACAGAGAATGAATTCGAGAAAAAACTACTATCAGACGTCATTCCTCCAAGTGATATCGGTGTTTCTTTCAGTGATATTGGGGCTTTGGAAA
upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 19
gtacaatcccctacatattgccgtgctttttggtgattcctcgagttatttactgaacactctacttacaagtcctttttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
||| | || | || || | | ||| | || | || | | | | | |||||||||||| || ||||| ||||||||||||| || ||| |||||| || ||||||| || || || ||| ||||||||||||||||||| |||| |
--gtaatattatgttacttaatttctttcttcccaagctgcctagtaagttccggattaagagttggtttactatactgtttcagGATGTTGTTACTGAGAACGAATTTGAGAAAAAACTGTTGTCGGATGTCATTCCACCTAGCGATATAGGTGTTTCCTTTGATGATATTGGAGCTCTGGAAA
upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 20
gtacaatcccctacatattgccgtgctttttggtgattcctcgagttatttactgaacactctacttacaagtcctttttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
||| | | | ||| |||| | || | |||||| | | | || | ||| | |||||||||||||| ||||| ||||||||||||||||||||| | | |||||||| ||||| ||||||||| || || |||||||||||||| ||| |||| |
gtaatttttgtaccttcatgcaactaatttttatc-tttaacaagttatattgattaaaatcaattta----tttccaatctcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATTCCACCATCTGACATTGGGGTCACATTTGATGATATTGGGGCCCTGGAAA
upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 19
-------------------------------gtacaatcccctacatattgccgtgctttttggt--gattcctcgagttatttactga-acactctacttacaagtcctt--tttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
| | || | ||| | | || | || | | | ||||||||| | | | | | || | || ||| ||||||||| || || ||||||||||||||||| | ||| | |||||||| ||||||| ||| |||||||| || ||||||||||||||||| || || |
gtaaagttgcagatgtctctataaattcatggctctattctctaaaaaaaacctcacaaattaatccagtctatgaagttatttaatcacatgttggaatttttatgccaaaatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA
upper sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
lower sequence: PP1S27_195V6.1 (Physcomitrella patens), 3'ss of exon 15
---------------gtacaatcccctacatattgccgtgctttttggtgattcct--cgagttatttactgaacactctacttacaa-gtcctttttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
|| || | | | | | || ||||||||||| | || | || || | | ||||||||||||||| |||||||| |||||||| | ||| ||| ||| ||||| |||||| |||| |||| || ||||| || | || || |||||||| |
tattgtgtacggtacgtggaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaatgctttcgagttattta---gaagtggtattgacgttgtggtgtggatcagGATGTTGTCACTGAGAATGAGTTTGAGAAGATGCTCTTGCCGGAGGTTATCCCACCTGATGAGCTTGGGGTAACCTTCGACCACATCGGTGCCTTGGATAMapped 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|67034427|gb|CO462977.1|CO462977EST: TGCTGCAAAGCATGCAAAGTGATAACAAGAGCTCGAAAAAATCACTGAAG GATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATA
genomic: TGCTGCAAAGCATGCAAAGTGATAACAAGAGCTCGAAAAAATCACTGAAGgtacaatccc ... tttttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATA
EST:
gi|60399121|gb|DN231935.1|DN231935EST: TGCTGCAAAGCATGCAAAGTGATAACAAGAGCTCGAAAAAATCACTGAAG GATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATA
genomic: TGCTGCAAAGCATGCAAAGTGATAACAAGAGCTCGAAAAAATCACTGAAGgtacaatccc ... tttttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATA
EST:
gi|211051788|gb|FL187606.1|FL187606EST: TGCTGCAAAGCATGCAAAG--ATAACAAGAGCTCGAAAAAATCACTGAAG GATGTTGTCACAGAGAATG
genomic: TGCTGCAAAGCATGCAAAGTGATAACAAGAGCTCGAAAAAATCACTGAAGgtacaatccc ... tttttctcagGATGTTGTCACAGAGAATG
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:
216CCTTAAGCATGGGCTCAACATGCTGCAAAGCATGCAAAGTGATAACAAGAGCTCGAAAAAATCACTGAAGgtacaatccc ... tttttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
Block sizes:
49 (upstream exon),
46 (downstream exon)
Score:
149CCTTAAGCATGGGCTCAACATGCTGCAAAGCATGCAAAGTGATAACAAGAGCTCGAAAAAATCACTGAAGgtacaatccc ... tttttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
Block sizes:
49 (upstream exon),
47 (downstream exon)
Score:
173CCTTAAGCATGGGCTCAACATGCTGCAAAGCATGCAAAGTGATAACAAGAGCTCGAAAAAATCACTGAAGgtacaatccc ... tttttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
Block sizes:
49 (upstream exon),
45 (downstream exon)
Score:
195CCTTAAGCATGGGCTCAACATGCTGCAAAGCATGCAAAGTGATAACAAGAGCTCGAAAAAATCACTGAAGgtacaatccc ... tttttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtgattcctcgagttatttactgaacactctacttacaagtcctttttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
tacttac putative branch site (score: 195)
tcctttttctc putative PPT
agttattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaatcccctacatattgccgtgctttttggtgattcctcgagttatttactgaacactctacttacaagtcctttttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA