Sequence
atgc intronic sequence ATGC exonic sequenceTGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattagaagctcttgctcggattatttgctatgctgatttctccaagaaccattcttggcaacaccagagaaacaatgaaacttgcccagtattcta...
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 5'ss of exon 5
TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattagaagctcttgctcggattatttgctatgctgatttctccaagaaccattcttggcaacaccagag-aaacaatgaa-acttgcccagtattcta-
|||||| ||||||||||| || || ||||||||||| || ||||||||||| |||||||| ||||| |||||||||||||| |||||||||||||||||||||||| | ||| ||||||| || || | | | | | || || |||| ||| | | | || | | |||| | | || |||||
TGCACTAAAACTTGAGTCTGTCCCGGACTGGATAGCAATCGTTGGAAGTGGATACATTGGGCTTGAATTCAGTGATGTATATACAGCTCTTGGAAGTGAGgtacatga-aagttcttgctgtgaataaattcaaggat-atggcttagagaatcatacagtg-agcatggaatcatgcaattattgcagaaacatggttctac
upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA15G15310.1 (Glycine max), 5'ss of exon 5
TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattagaagctcttgctcggattatttgctatgctgatttctccaagaaccattcttggcaacaccagagaaac-aatgaaacttgcccagtattcta-----------------------------------------------------------------------------------------------------
|||||| ||||| ||| | ||||| || |||||||| ||||| ||||||||||| ||||| ||||| |||||||||||||| || || ||||||||||||| ||| | ||| | ||||| | | | |||||| || | || | || ||| ||| | | | || ||| | ||
TGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGATGTATATACGGCCCTTGGAAGTGAGg-----tagtacttctcttctgatatatttttttttatcctttctc----aattgtattttgtt-catgagaagaactgacaatagttttccaatttttcttttatgacgtttgaaagttttttatattatctcattgtttgaaaagttagaaacctaatttgtgcagaagagatatagttggtaataatggtactctgcag
upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G37050.2 (Glycine max), 5'ss of exon 5
TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattagaagctcttgctcggattatttgctatgctgatttctccaagaaccattcttggcaacaccagagaaacaatgaaacttgcccagtattcta
||||| ||||| || || ||||| || |||||||| ||||| |||||||| || ||||| ||||| |||||||||||||| ||||| ||||||||||||||| | | ||| ||| | || |||| | |||||| || | ||| ||| || | | | | |
CGCACTCAAACTGGAATCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGATGTATATACAGCACTTGGAAGTGAGgtagcacatctttgtgaattttgatactttttctttctcttttcattaccttttgttcttgagaaatatttacaaataatcaatcctatcatttgacatc
upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 5
TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattagaagctcttgctcggattatttgctatgctgatttctccaagaaccattcttggcaacaccagagaaacaatgaaac---ttgcccagtattcta----
||||| ||||| ||||| ||||| || |||||||| ||||| |||||||| || ||||| ||||| |||||||||||||| ||||| ||||||||||||| ||| | |||| | | | ||| | || |||| | |||||| || | ||| ||| | | | || |
CGCACTCAAACTGGAGTCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGATGTATATACAGCACTTGGAAGTGAGg-----tagcacatctttgtgatactgtttcttt--cttttttcattaccttttgttcttgataaatatttataaataatcgatcccttcatttgacatcagaaata
upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 5'ss of exon 5
TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattagaagctcttgctcggattat-ttgctatgct--gatttctccaagaaccattcttggcaacaccagagaaacaatgaaacttgcccagtattcta
||| ||||| | ||||| || || || ||||| || ||||| ||||||||||| ||||| ||||||||||||||||| |||||||||||||||||||||||| | || | | || | || || || || | | || || | | | |||| | | || || | || | | | ||||
TGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgta-acatgatgtttctgtactaatgatattactttagtacgactttgtgatgttgtgtccttgtacttgagattgtaataactgcaattagc-aatgttct-
upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 5
TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgta-cattagaagctcttgctcggattatttgctatgctgatttctccaagaaccattcttggcaacaccagagaaacaatgaaacttgcccagtattcta----
|||| ||||| | ||||| ||||| |||||||| || || || ||||||||||| || || ||||||||||||||||| ||||| || ||||||||||||||| |||| | | |||| || |||||| ||| | | | || || || | || | | | | |
TGCATTGAAATTGGAGTCCGTTCCTGACTGGATTGCGATAGTAGGAAGTGGTTATATCGGTCTTGAGTTCAGTGATGTTTACACGGCCCTTGGAAGTGAGgtaacattttgattttgtgct--aatgatttgc---actggtgtgatagtgtgttgttttttgcgttctctttagttttctgttttctctcaatagtaacaaaag
upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 5
TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgta---cattagaagctcttgctcggattatttgctatgctgatttctccaagaaccattcttggcaacaccagagaaacaa--tgaaacttgcccagtattcta
||| || ||||| ||||| ||||| || |||||||| ||||| ||||||||||| ||||| ||||| ||||||||||| || ||||| ||||||||||||||| || | | ||||| || | || | |||| ||| ||| | ||| ||| | | || | | | ||
TGCGCTCAAACTGGAGTCTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAGgtagcatcttctttatagtcattgcgattacagtttaaatttatataaatgagaa--atttcaatcaatagt-gagttacagcttagatctggtgctaaaatc--
upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv14s0060g01410.t01 (Vitis vinifera), 5'ss of exon 4
TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgta--cattagaagctcttgctcggattatttgctatgctgatttctccaagaaccattcttggcaacaccagagaaacaatgaaacttgcccagtattcta-
||||| ||| | || | |||| || |||||||| |||||||| ||||| |||||||| |||||||| ||||||||||| | || ||||||||||||||| || | | || | | | || | | | ||||| || | | || | | | | | || | || |||
AGCACTTAAATTGGAATTTATTCCTGATTGGATAGCCATTGTTGGCAGTGGCTACATTGGTCTTGAGTTTAGTGATGTATATATGGCACTTGGAAGTGAGgtaggcacaatattatcatattaaagacactt-cattagtaatttcattttcaa--actgaaagctgtggaaaatctttagttcatctatacttatactctta
upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 5'ss of exon 5
TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgta--cattagaagctcttgctcggattatttgctatgctgatttctccaagaaccattcttggcaacaccagagaaacaatgaaacttgcccagtattcta-
||||| ||| | || | ||||| || |||||||| |||||||| ||||| |||||||| |||||||| ||||||||||| ||||| ||||||||||||||| || | | || | | || || | | || | |||| || | | | | | || | || |||
AGCACTTAAATTGGAATTTGTTCCCGATTGGATAGCCATTGTTGGCAGTGGCTACATTGGTCTTGAGTTTAGTGATGTATATACAGCACTTGGAAGTGAGgtaggcacaatattatcatattaaagatacttcattagtaatttcattttcgaactga---aagctgtggaaaatctttagttcatctgtacttatactctta
upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattagaagctcttgctcggattatttgctatgctg-----atttctccaagaaccattcttggcaacaccagagaaacaatgaaacttgcc-cagtattcta-----------
||| ||||| || |||| | ||||||||||| || ||||||||||||||||||||||| ||||||||||| ||||| || || || ||||||||||||||| || | || |||||| | || | | | | || | | | || || | || | || | | | ||||
TGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGATGTCTATACTGCCCTTGGAAGTGAGgta------aaatttccttgcgcattattgacaataaaataaaagtggatgtgtggagtgcgtgtgtaattatctgacaataattggagctgacttcccttttctgtgggcttgcag
upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattagaagctcttgctcggattatttgctatgctgatttctccaagaaccattcttggcaacaccagagaaacaatgaaacttgcccagtattcta--------------------
|| |||| | |||| ||||||||||||| || || ||||| || ||||||||||| || |||||||||||||||||||||||||| ||||| ||||| | | | | | ||| || || | | ||| | | | ||| | | | || | | | || | | |
CGCTTTGAAGTTAGAGTGGATTCCAGACTGGATTGCGATCGTTGGCAGCGGTTACATTGGTCTAGAGTTCAGTGATGTATACACAGCTCTCGGAAGCGAGgtcagtaaccgtttgtctcacggtctaggagcatttttattttattctattttttcactttgtcgtatatcttcatcacttgtatggactcacaagttgacctcttttcgtgcccggcag
upper sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattagaagctcttgctcggattatttgc-----tatgctgatttctccaagaaccattcttggcaa--caccagagaaacaatgaaacttgcccagtattcta---------
||| |||| || |||| |||| |||||||| ||||||| ||||||||||||||||| ||||||||||||||||| ||||| || |||||||| |||||||| | | | | | ||||| || || | | | | | || || || | | | || || | | |
TGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGATGTTTACACTGCCCTTGGAAGCGAGgtacagttttattgaaaggacacaatatttttaaaaataaaatggatatattgggttctagttttaaaaagttgtcatctagtggagcttattttcctcttgctgtgggttggcagMapped 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|211514676|gb|FL210540.1|FL210540EST: GGTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAG GTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAA
genomic: GTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattaga ... aattgggcagGTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAA
EST:
gi|211056151|gb|FL241561.1|FL241561EST: GTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAG GTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAA
genomic: GTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattaga ... aattgggcagGTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAA
EST:
gi|67016819|gb|CO445568.1|CO445568EST: GTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAG GTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAA
genomic: GTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattaga ... aattgggcagGTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAA
EST:
gi|6536537|gb|AW224850.1|AW224850EST: GGTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAG GTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAA
genomic: GTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattaga ... aattgggcagGTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAA
EST:
gi|31354606|gb|CD438963.1|CD438963EST: GTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAG GTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAA
genomic: GTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattaga ... aattgggcagGTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAA
EST:
gi|6626525|gb|AW258057.1|AW258057EST: GGTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAG G-TACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAA
genomic: GTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattaga ... aattgggcagGTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAA
EST:
gi|211517024|gb|FL210545.1|FL210545EST: GTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTTGGAAGTGAG GTTACTTTTGTTGAAGCTCTTGA
genomic: TTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTT-GGAAGTGAGgtacattaga ... aattgggcagGTTACTTTTGTTGAAGCTCTTGA
EST:
gi|32932110|gb|CF036922.1|CF036922EST: ACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAG GTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAA
genomic: ACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattaga ... aattgggcagGTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAA
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:
133TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattaga ... aattgggcagGTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTTCTTATCAATCCTCGGAAAATTGACT
Block sizes:
45 (upstream exon),
45 (downstream exon)
Score:
112TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattaga ... aattgggcagGTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTTCTTATCAATCCTCGGAAAATTGACT
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
79TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattaga ... aattgggcagGTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTTCTTATCAATCCTCGGAAAATTGACT
Block sizes:
49 (upstream exon),
45 (downstream exon)
Score:
214TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattaga ... aattgggcagGTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTTCTTATCAATCCTCGGAAAATTGACT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattagaagctcttgctcggattatttgctatgctgatttctccaagaaccattcttggcaacaccagagaaacaatgaaacttgcccagtattcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG