Sequence
atgc intronic sequence ATGC exonic sequence...aatgcgtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattggcggcgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G123667_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 2
---aatgcgtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattggcggcgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
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ccaaaaactttttaccacca--ccactcgcatgcattccacatcaatcttgatcactttgctaataatttcagttttttttttggttaattttt-ttttgcagTTGGATGATTGGGTGTTGTGCCGAATCTACAACAAGAAGGGAGTGATCGAGAGGTACGACACGGTGGACGCCGGCGAGGACGTGAAGCCGGCGGCGGCGG
upper sequence: GRMZM2G123667_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G26480.1 (Glycine max), 3'ss of exon 2
aatgcgtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattggcgg--cgcttaaccatga--agtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACG-GCGACGGCGCCGTGGCCGAAG
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----ggaaattattcgttctttcttatctctattgaagttagggatatgagaaattgaaaattaaaaaaatgtttgcacatgattgttgtttctgattatgcagCTGGATGACTGGGTGCTGTGTCGAATTTACAACAAGAAAGGTGCAATTGAGAAGCAGCAACCAGCAC-CGCCACCACCGAGTGGTGTCCACAAAATTGAAT
upper sequence: GRMZM2G123667_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA14G24220.1 (Glycine max), 3'ss of exon 2
--aatgcgtagtaaaaaaaacccaatcagcttagtctgacttttcac-tgggatttcgcgtggattggcggcgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG------
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ttcgttcttatcttagggatatcggaaattaaaaattgaagattaaaatatgtgtgcacatg-attgctgac--ttaattttgatgatttctgatttttgcagCTGGATGACTGGGTGCTGTGCCGAATTTACAACAAGAAAGGTGCAATTGAAAAGCA----ACAACTACCACCACCGA--GTGGGGTCCGCAAAATTGAATGTTCCG
upper sequence: GRMZM2G123667_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G11970.1 (Glycine max), 3'ss of exon 2
aatgcgtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcg--tggattggcggcgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG---
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tat-ctctctcacctgcctccgattgcaatacttataataataaatgaaaatgaagaaataatcttacggtggttg-tgatttttttttttttttgtcgcagTTGGATGATTGGGTGCTTTGCCGTATTTACAACAAGAAGGGCACGATCGAGAA--ACTGCA-ACCAAGCAGCGATGTTGCTCATAGCCGAAATATCGAATCCT
upper sequence: GRMZM2G123667_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S140_93V6.1 (Physcomitrella patens), 3'ss of exon 2
-aatgcgtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattg---gcggcgcttaaccatgaagtgtctactgtct-tgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
||| || | | || | | || | || || ||| | | || | | ||||| || ||||| || || | | | | | |||| ||||||| |||||| |||||||||||||||| |||| | |||| | || | | || | || || | |
ggatg-gtgctgtcactaattctgt--gcacattcc-acacgtcaatcgtatctgaaggcgattgttcatggtgctta-tgattttgtttacattctgtgcgcagTTGGATGATTGGGTGTTGTGCCGGATCTACAAAAAGAGTACAAATGCACAGCGTACTGGCAAGGAGCGTGATAGCTCTTCTTGCGTCGAAGAG-------
upper sequence: GRMZM2G123667_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ36823 (Selaginella moellendorffii), 3'ss of exon 1
------------------------------------------------aatgcgtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattggcggcgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
|| |||||||| || || || || | | ||| ||| ||| | ||| || | || | | ||||||||||| ||||||||||||||||||||||||| ||||||
gtaagtttcaattcctccaagtagttgcataagtcctgcatattggggaaaaaaacaaaaaaaaaaaaaaaaaagagagctcgagctcatgagtggtattaaaaaccgatggct--tactttggcaagctgttcttctttcgttgcagCTGGACGACTGGGTGCTGTGCCGGATCTACAGAAAGAAGACA----------------------------------------------------------
upper sequence: GRMZM2G123667_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ27849 (Selaginella moellendorffii), 3'ss of exon 1
---------------------------------------------------------aatgcgtagtaaaaaaaacccaatcagcttagtctga-cttttcactgggatttcgcgtggattggcggcgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
|| | |||||||| || || || || | | ||| ||| ||| | ||| || | || | | ||||||||||| ||||||||||||||||||||||||| ||||||
gtaagtttcaattcctccaagtagttgcatccagtcctgcatattggggaaaaaaacaaaaaaaacaaaaaaaaaaaaaaaagaaagagcgagagctcgtgagtggtattaaaaaccgatggct--tactttggcaagctgttcttctttcgttgcagCTGGACGACTGGGTGCTGTGCCGGATCTACAGAAAGAAGACA----------------------------------------------------------
upper sequence: GRMZM2G123667_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ31748 (Selaginella moellendorffii), 3'ss of exon 1
aatgcgtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattggcggcgcttaaccatga--agtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
||| | | | |||| | | || || ||| || | | || |||||||| ||||||||||||||||| || ||||| ||||||
--------------------------------------gtttgaaagccgctgactagatattgactgtttttgactatgtttgacttccatgttttttcagCTGGACGACTGGGTGCTGTGCCGAATTTACAAAAAGAAG-------------------------------------------------------------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|91048064|gb|EB158482.1|EB158482EST: ACGTCGACCGCTCGGCCGCCGCACGCAAGAAGACCAACAACGCGCTCAGG CTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAG
genomic: ACGTCGACCGCTCGGCCGCCGCACGCAAGAAGACCAACAACGCGCTCAGGgtaattcact ... tgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAG
EST:
gi|89251024|gb|DY622810.1|DY622810EST: ACGTCGACCGCTCGGCCGCCGCACGCAAGAAGACCAACAACGCGCTCAGG CTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAG
genomic: ACGTCGACCGCTCGGCCGCCGCACGCAAGAAGACCAACAACGCGCTCAGGgtaattcact ... tgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgggatttcgcgtggattggcggcgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
gcttaac putative branch site (score: 3)
ctgtctt putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgcgtagtaaaaaaaacccaatcagcttagtctgacttttcactgggatttcgcgtggattggcggcgcttaaccatgaagtgtctactgtcttgcagCTGGATGACTGGGTGCTGTGCCGGATCTACAACAAGAAGGGTGTTATCGAGCGGTACGACACAGTGGACGACGACGACGGCGACGGCGCCGTGGCCGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA