Sequence
atgc intronic sequence ATGC exonic sequence...tatgcctttacatttgtggtgctgctttatgctaatgttttggttgaaaaatgttctttggtttataaaattcttataatttctgattcgtggtgttataGATGTGGTGAGGGATGATCCAACAAATAATGTGCCAGACAATATATTTTCAAAACTTGGAGTGCATCTTCACAGGAGGGATCAACACCCTCTTGGGATAC
Basic information
species | Glycine max |
transcript | GLYMA18G52890.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0027g01150.t01 (Vitis vinifera), 3'ss of exon 2
tatgcctttacatttgtggtgctgctttatgctaatgttttggttgaaaaatgttctttggtttataaaatt--cttataatttctgattcgtggtgttataGATGTGGTGAGGGATGATCCAACAAATAATGTGCCAGACAATATATTTTCAAAACTTGGAGTGCA---TCTTCACAGGAGGGATCAACACCCTCTTGGGATAC
| || ||| | | | | || || || || || | ||| | || ||| || | || || || || |||||||||||||||||||||| ||||| ||||| || || || ||||| ||||||||| |||| ||||||||||||||||||| |||| |||| ||
---gttattctattctgaatatttggtaaaattagaattcatgtactgaacctttttcaagttcttttggttggcttgatatatttggttgtggggtttgtagATGTGGTGAGGGATGATCCTACAAACAATGTCCCGGATGCAATTTTTTCGAAACTTGGAATGCAGCTTCTTCACAGGAGGGATCAAAACCCAATTGGAAT--
upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0027g01190.t01 (Vitis vinifera), 3'ss of exon 1
tatgcctttacatttgtggtgctgctttatgctaatgttttggttgaaaaatgttctttggtttataaaatt--cttataatttctgattcgtggtgttataGATGTGGTGAGGGATGATCCAACAAATAATGTGCCAGACAATATATTTTCAAAACTTGGAGTGCATCTTCACAGGAGGGATCAACACCCTCTTGGGATAC-
| || ||| | | | | || | || || || | ||| | || ||| || | || || || || |||||||||||||||||||||| ||||| ||||| || || || |||| ||||||||| |||| ||||||||||||||||||||||| |||| || |
---gttattctattctgaatatttggtaaaattagaactcatgtactgaacctttttcaagttcttttggttggcttgatatatttggttgtggggtttgtagATGTGGTGAGGGATGATCCTACAAACAATGTCCCGGATGCAATTTTTTTGAAACTTGGAATGCAGCTTCACAGGAGGGATCAACACCCAATTGGAATTCT
upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0027g01190.t01 (Vitis vinifera), 3'ss of exon 1
tatgcctttacatttgtggtgctgctttatgctaatgttttggttgaaaaatgttctttggtttataaaatt--cttataatttctgattcgtggtgttataGATGTGGTGAGGGATGATCCAACAAATAATGTGCCAGACAATATATTTTCAAAACTTGGAGTGCATCTTCACAGGAGGGATCAACACCCTCTTGGGATAC-
| || ||| | | | | || | || || || | ||| | || ||| || | || || || || |||||||||||||||||||||| ||||| ||||| || || || |||| ||||||||| |||| ||||||||||||||||||||||| |||| || |
---gttattctattctgaatatttggtaaaattagaactcatgtactgaacctttttcaagttcttttggttggcttgatatatttggttgtggggtttgtagATGTGGTGAGGGATGATCCTACAAACAATGTCCCGGATGCAATTTTTTTGAAACTTGGAATGCAGCTTCACAGGAGGGATCAACACCCAATTGGAATTCT
upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 1
tatgcctttacatttgtggtgctgctttatgctaatgttttggttgaaaaatgttctttggtttataaaatt--cttataatttctgattcgtggtgttataGATGTGGTGAGGGATGATCCAACAAATAATGTGCCAGACAATATATTTTCAAAACTTGGAGTGCATCTTCACAGGAGGGATCAACACCCTCTTGGGATAC-
| || ||| | | | | || || || || || | ||| | || ||| || | || || || || |||||||||||||||||||||| ||||| ||||| || || || |||| ||||||||| |||| ||||||||||||||||||||||| |||| || |
---gttattctattctgaatatttggtaaaattagaattcatgtactgaacctttttcaagttcttttggttggcttgatatatttggttgtggggtttgtagATGTGGTGAGGGATGATCCTACAAACAATGTCCCGGATGCAATTTTTTTGAAACTTGGAATGCAGCTTCACAGGAGGGATCAACACCCAGTTGGAATTCT
upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 1
tatgcctttacatttgtggtgctgctttatgctaatgttttggttgaaaaatgttctttggtttataaaatt--cttataatttctgattcgtggtgttataGATGTGGTGAGGGATGATCCAACAAATAATGTGCCAGACAATATATTTTCAAAACTTGGAGTGCATCTTCACAGGAGGGATCAACACCCTCTTGGGATAC-
| || ||| | | | | || || || || || | ||| | || ||| || | || || || || |||||||||||||||||||||| ||||| ||||| || || || |||| ||||||||| |||| ||||||||||||||||||||||| |||| || |
---gttattctattctgaatatttggtaaaattagaattcatgtactgaacctttttcaagttcttttggttggcttgatatatttggttgtggggtttgtagATGTGGTGAGGGATGATCCTACAAACAATGTCCCGGATGCAATTTTTTTGAAACTTGGAATGCAGCTTCACAGGAGGGATCAACACCCAGTTGGAATTCT
upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0027g01380.t01 (Vitis vinifera), 3'ss of exon 1
tatgcctttacatttgtggtgctgctttatgctaatgttttggttgaaaaatgttctttggtttataaaatt--cttataatttctgattcgtggtgttataGATGTGGTGAGGGATGATCCAACAAATAATGTGCCAGACAATATATTTTCAAAACTTGGAGTGCATCTTCACAGGAGGGATCAACACCCTCTTGGGATAC-
| || ||| | | | | || || || || || | ||| | || ||| || | || || || || |||||||||||||||||||||| ||||| ||||| || || || || || ||||||||| |||| ||||||||||||||||||||||| |||| || |
---gttattctattctgaatatttggtaaaattagaattcatgtactgaacctttttcaagttcttttggttggcttgatatatttggttgtggggtttgtagATGTGGTGAGGGATGATCCTACAAACAATGTCCCGGATGCAATTTTGTCGAAACTTGGAATGCAGCTTCACAGGAGGGATCAACACCCAATTGGAATTCT
upper sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 1
tatgcctttacatttgtggtgctgctttatgctaatgttttggttgaaaaatgttctttggtttataaaattcttataatttctgattcgtggtgtt-ataGATGTGGTGAGGGATGATCCAACAAATAATGTGCCAGACAATATATTTTCAAAACTTGGAGTGCATCTTCACAGGAGGGATCAACACCCTCTTGGGATAC-
| ||| |||| | | | | ||||| || |||||| || | | || | | | | | | | | | | |||||||| ||||||||||||| || ||||||||||| ||||| || || | || ||||||||||||||| |||| ||||||||||||||||||||||| |||| || |
--ttttttttaattttttgggttattttattctggatatttggtaaaattagaattcatgttcttttgattggcttgattcatttggttgtggtgtttgtagATGTGGTGAGAGACGATCCAACAAACAATGTCCCGGATGAAATTTTTTCAAAACTTGGAATGCAGCTTCACAGGAGGGATCAACACCCAATTGGAATTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaaatgttctttggtttataaaattcttataatttctgattcgtggtgttataGATGTGGTGAGGGATGATCCAACAAATAATGTGCCAGACAATATATTTTCAAAACTTGGAGTGCATCTTCACAGGAGGGATCAACACCCTCTTGGGATAC
ttctgat putative branch site (score: 3)
ttctttggtttataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgcctttacatttgtggtgctgctttatgctaatgttttggttgaaaaatgttctttggtttataaaattcttataatttctgattcgtggtgttataGATGTGGTGAGGGATGATCCAACAAATAATGTGCCAGACAATATATTTTCAAAACTTGGAGTGCATCTTCACAGGAGGGATCAACACCCTCTTGGGATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
tatgcct
- - - - - - - tgtggtg
- - - - - - - - - - - - -tttatgc
- - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgattc