Sequence
atgc intronic sequence ATGC exonic sequencegtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g38790.1 (Oryza sativa), 3'ss of exon 5
------------------gtatgcttctaaccatcatctatatgtcttttagtttacttgt-gcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG----------------------------------------------
| | || | | |||| || | || ||| || || ||| ||| | | |||||| | | | | ||||||| | |||| || ||| |||||||||||||||| |||||| | || ||||||||||||||||||||||||||||||
gtatattttccatcctctctttagttgttattctcat-tagagatcatttggtatatatgttacattactagatatgagtttgagg---gttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAGGTAAGTTCTGATTTTTATAATTTTATATCTGTAATATTAATGATAT
upper sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g38790.3 (Oryza sativa), 3'ss of exon 5
------------------gtatgcttctaaccatcatctatatgtcttttagtttacttgt-gcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG
| | || | | |||| || | || ||| || || ||| ||| | | |||||| | | | | ||||||| | |||| || ||| |||||||||||||||| |||||| | || ||||||||||||||||||||||||||||||
gtatattttccatcctctctttagttgttattctcat-tagagatcatttggtatatatgttacattactagatatgagtttgagg---gttatctcaaatatttgttgacttgtgtagGAGGAAAGAAGATTGTCGCTACCCAAGTATCAGGTGCATGATGAAACTAGCCAG
upper sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G34280.1 (Glycine max), 3'ss of exon 5
gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG
|| | | | || | | | | | ||| | | | | | ||| |||| | | | | || | |||||||||||||||| |||| |||||||| ||||||||||||||||||| |||||||
--gtgagttgtgttcttgagaaaatatgtagtgttccatttgactactgttgtttcttg-------gttggtaatattatgatgct--tggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG
upper sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G05390.1 (Glycine max), 3'ss of exon 5
gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG----------------------------------------------
|| | | | || | | | || | ||| | || | | ||| ||| |||| | | | | || | |||||||||||||||| |||| |||||||| ||||||||||||||||||| |||||||
--gtgtgttgtgttcttgagaaaatatgtagtgtttcatttg---actgctgttgtttcttg----gttggtaatgttatgatgct--tggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAGGTAAGTCATACTACCTCTTTAATAGATGGAGTTGCTTTCACATCTA
upper sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G05390.2 (Glycine max), 3'ss of exon 5
gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG
|| | | | || | | | || | ||| | || | | ||| ||| |||| | | | | || | |||||||||||||||| |||| |||||||| ||||||||||||||||||| |||||||
--gtgtgttgtgttcttgagaaaatatgtagtgtttcatttg---actgctgttgtttcttg----gttggtaatgttatgatgct--tggttactgtagGAGGAAAGAAGAATGTCTTTGCCAAAATATCAGGTGCATGATGAAAGTAGCCAG
upper sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv01s0011g01240.t01 (Vitis vinifera), 3'ss of exon 5
---gtatgcttctaaccatca-tctata-tgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG
|| |||| | | || || |||||||| || | | | |||| | || || ||| | | | || |||| ||||||||||||| |||| || ||||| ||||||||||||||||||||||||
gtcagttgtttctgaatgcaactccatgctgtctttttgta-atgcagctgtggttatatgttat-------tttatattttggtatggtttacaaaatttgcagGAGGAAAGAAGAATGTCATTAATGAAGTACCAGGTGCATGATGAAACTAGCCAG
upper sequence: GRMZM2G081812_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv03s0017g02160.t01 (Vitis vinifera), 3'ss of exon 5
gtatgcttctaaccatcat-ctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtct-tttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG
|| | | || | | | || |||| | | ||| || || | | || || || | | | | |||| | | | | | |||||||||||||| |||| || | ||||||||||||||||||||||||||||||
gttagttgttagttacctttctggatgtatcatgccaatcttttggatgctgtactttggtttaac-----acactttaaattgtgtttgaaatatctacagGAGGAAAGAAGGATGTCATTACTGAAGTATCAGGTGCATGATGAAACTAGCCAGMapped 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|60394945|gb|DN227814.1|DN227814EST: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATG GAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
genomic: CAGCTACGAATGAGGTATATCTGGTGTGGGATGATGAAGCAATGTCAATGgtatgcttct ... tcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG
tgttaat putative branch site (score: 3)
ttttttgctgtctttt putative PPT
atatatgattgaaatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcttctaaccatcatctatatgtcttttagtttacttgtgcatagcgatatatgattgaaatgttaataatctcaattttttgctgtcttttgtagGAGGAAAGAAGGTTGTCGTTGCCAAAGTATCAGGTGCATGATGAAACTAGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG