Sequence
atgc intronic sequence ATGC exonic sequencegtgggtaatgggttcctctcatgtttttccatttgaatgaaatgctgttaatcaaagttatgtgacatgagtatattataacactgttgtctgttttcttttcgtggtgttgccatttgaaaaaccatcattcagATCATTGGTGAAATATCTGTGTCTGGTGCAACATATAAAACGATGGAGTTTGTTGGGACAACAATTGAAAGTTTAAGT
Basic information
species | Glycine max |
transcript | GLYMA20G34160.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 6
gtgggtaatgggttcctctcatgtttttccatttgaatgaaatgctgttaatcaaagttatgtgacatgagtatattataacactgttgtctgttttct----tttcgtggtgttgccatttgaaaaaccatcatt--cagATCATTGGTGAAATATCTGTGTCTGGTGCAACATATAAAACGATGGAGTTTGTTGGGACAACAATTGAAAGTTTAAGT
|| || | | ||||||| | || ||| | | | ||| | | | | || || | | ||||| |||||||| || ||||| ||||| |||||||| ||| | |||||||||||||| |||| | |||||| ||| |
---------------------------------------------------gtaagactacaaaatacttgtatatttttctgtacttatctttctaccagcattttctaatagctcatcctcaataattgctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 7
gtgggtaatgggttcctctcatgtttttccatttgaatgaaatgctgttaatcaaagttatgtgacatgagtatattataacactgttgtctgttttcttttcgtggtgttgccatttgaaaaaccatcattcagATCATTGGTGAAATATCTGTGTCTGGTGCAACATATAAAACGATGGAGTTTGTTGGGACAACAATTGAAAGTTTAAGT
| ||| || | ||||||| | | ||| | ||| | ||| | | ||| | | | | | | ||||| |||||||| || || || ||||||||||| || ||| |||||||||||||||| |||| | |||||| |||
---------------------------------------gtaagcttacaagctgtgttatgtttgttccttcccttaggatctacctgta-accatgacttcttattcttgttaatcggta------cttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 7
gtgggtaatgggttcctctcatgtttttccatttgaatgaaatgctgttaatcaaagttatgtgac-atgagtatattataacactgttgtctgttttcttttcgtggtgttgccatttgaaaaaccatcattcagATCATTGGTGAAATATCTGTGTCTGGTGCAACATATAAAACGATGGAGTTTGTTGGGACAACAATTGAAAGTTTAAGT
| || || | | |||| | || | | | || | || | || | | | | | ||| || || | | | |||| ||||||||||||||||| |||||||||| || || ||||||||||| ||| ||||| || |||||| | |||
--------------------------------gcagtctctaaattgatagtttac-ttatatagtgattactcttttgggattctatctggcgtccttcatctg-gatattgaacttgcttcaaactttgt--agATTATTGGTGAAATATCTGTTGCTGGTGCAACTTACAAGACGATGGAGTTCAGTGGTACAACTATCGAAAGTCTGAGT
upper sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ32611 (Selaginella moellendorffii), 3'ss of exon 6
gtgggtaatgggttcctctcatgtttttccatttgaatgaaatgctgttaatcaaagttatgtgacatgagtatattataacactgttgtctgttttcttttcgtggtgttgccatttgaaaaaccat-cattcagATCATTGGTGAAATATCTGTGTCTGGTGCAACATATAAAACGATGGAGTTTGTTGGGACAACAATTGAAAGTTTAAGT----------------------
|| | || | | | | | | || | | || || || || | || ||||||||||| || || |||| || ||||||||||| ||| | |||||||||||||||||| | | ||| || | |
----------------------------------------------------------------gtgtgtttggatcttta-gcgagagctggctccctgtacttgaagtacttatatgcgcgttgaggcacacagATCATTGGAGAGATCACTGTTTCCGGTGCAACATACAAATCAATGGAGTTTGTTGGGACAGCTGTAGAACGTATGACGGTCAGTTCTTTTTCCCCTTACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acactgttgtctgttttcttttcgtggtgttgccatttgaaaaaccatcattcagATCATTGGTGAAATATCTGTGTCTGGTGCAACATATAAAACGATGGAGTTTGTTGGGACAACAATTGAAAGTTTAAGT
ttataac putative branch site (score: 2)
atttgaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggtaatgggttcctctcatgtttttccatttgaatgaaatgctgttaatcaaagttatgtgacatgagtatattataacactgttgtctgttttcttttcgtggtgttgccatttgaaaaaccatcattcagATCATTGGTGAAATATCTGTGTCTGGTGCAACATATAAAACGATGGAGTTTGTTGGGACAACAATTGAAAGTTTAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA