Sequence
atgc intronic sequence ATGC exonic sequencegtaatttgcctggaaaacaaaatttcacacacatgtactaagatctttaaattttacataatatgaaatgtaatgtaagtatctaacatacaaatccatgtgtagGTTTTGATGGGGTTGAGATCCACGGTGCTCATGGCTACTTACTTGAGCAATTCATTAAAGACAAAGTGAATGATCGAAGTGATGGATATGGTGGATCCCT
Basic information
species | Glycine max |
transcript | GLYMA19G09320.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02020.t01 (Vitis vinifera), 3'ss of exon 4
gtaatttgcctggaaaacaaaatttcacacacatgtactaagatctttaaattttacataatatgaaatgt--aatgtaagtatctaacatacaaatccatgtgtagGTTTTGATGGGGTTGAGATCCACGGTGCTCATGGCTACTTACTTGAGCAATTCATTAAAGACAAAGTGAATGATCGAAGTGATGGATATGGTGGATCCCT
| | || | | | || || | | || | | | | | | | ||| || | | || | || || ||||||||||||||| || |||||||| || |||||||||||| ||||||| || ||||| |||||| | || |||||||||| ||| |||||||||||||||
----ccattcccaccattgaattattggattttagtcttatggttttgtgaatgaagtcacttcagtttctttgatgcaataacattacttgt---tcaatatgtagGTTTTGATGGAGTCGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
upper sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02080.t01 (Vitis vinifera), 3'ss of exon 4
---gtaatttgcctggaaaacaaaatttcacacacatgtactaagatctttaaattttacataatatgaaatgtaatgtaagtatctaacatacaaatccatgtgtagGTTTTGATGGGGTTGAGATCCACGGTGCTCATGGCTACTTACTTGAGCAATTCATTAAAGACAAAGTGAATGATCGAAGTGATGGATATGGTGGATCCCT
| | | | | |||| | || |||||| ||| | | | | ||| || | | || | || || |||||| |||||||| ||||||||||| || |||||||||||| ||||||| || ||||| |||||| | || || ||||||| |||| |||||| ||||||||
ctattgaaccatttcgtggatgtaattcc-----caaatactaaaccgcacttgatttgcccttcaatttctttgatgcaataacattacttgt---tcaatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAACGATCGAACTGATAAATATGGCGGATCCCT
upper sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02010.t01 (Vitis vinifera), 3'ss of exon 4
gtaatttgcctggaaaacaaaatttcacacacatgtactaagatctttaaattttacataatatgaaatgtaatgtaagtatctaacatacaaatccatgtgtagGTTTTGATGGGGTTGAGATCCACGGTGCTCATGGCTACTTACTTGAGCAATTCATTAAAGACAAAGTGAATGATCGAAGTGATGGATATGGTGGATCCCT
| ||| | || | ||| || | | || | || || ||| | | ||| || | | | || | ||||||||||||| ||||||||||| || ||||||||||| ||||||| || ||||| |||||| | || |||||||||| || ||||||||||| |
------------gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgatgcactaatgataatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGAGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCACA
upper sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02070.t01 (Vitis vinifera), 3'ss of exon 4
gtaatttgcctggaaaacaaaatttcacacacatgtactaagatctttaaattttacataatatga--aatgtaatg-taagtatctaacatacaaatccatgtgtagGTTTTGATGGGGTTGAGATCCACGGTGCTCATGGCTACTTACTTGAGCAATTCATTAAAGACAAAGTGAATGATCGAAGTGATGGATATGGTGGATCCCT
| ||| | || | ||| || | | || | || || ||| | ||| | || | | || | ||| | || | ||||||||||||| ||||||||||| || ||||||||||| ||||||| || ||||| |||||| | || |||||||||| || ||||||||||||||
------------gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgatgcactgatgataatattgtttac---ccaatatatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCCCT
upper sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02060.t01 (Vitis vinifera), 3'ss of exon 4
gtaatttgcctggaaaacaaaatttcacacacatgtactaagatctttaaattttacataatatgaaatgt--aatgtaagtatctaacatacaaatccatgtgtagGTTTTGATGGGGTTGAGATCCACGGTGCTCATGGCTACTTACTTGAGCAATTCATTAAAGACAAAGTGAATGATCGAAGTGATGGATATGGTGGATCCCT
| | || | | | || || | | || | | | | | | | ||| || | | || | || || ||||||||||||||| ||||||||||| || |||||||||||| ||||||| || ||||| |||||| | || |||||||||| ||| |||||||||||||||
----ccattcccaccattgaattattggattttagtcttatggttttgtgaatgaagtcacttcagtttctttgatgcaataacattacttgt---tcaatatgtagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
upper sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02050.t01 (Vitis vinifera), 3'ss of exon 3
gtaatttgcctggaaaacaaaatttcacacacatgtactaagatctttaaattttacataatatga--aatgtaatg-taagtatctaacatacaaatccatgtgtagGTTTTGATGGGGTTGAGATCCACGGTGCTCATGGCTACTTACTTGAGCAATTCATTAAAGACAAAGTGAATGATCGAAGTGATGGATATGGTGGATCCCT
| ||| | || | ||| || | | || | || || ||| | ||| | || | | || | ||| | || | ||||||||||||| ||||||||||| || ||||||||||| ||||||| || ||||| |||||| | || |||||||||| || ||||||||||| ||
------------gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgatgcactgatgataatattgtttac---ccaatatatagGTTTTGATGGAGTTGAGATCCATGGAGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCACT
upper sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02040.t01 (Vitis vinifera), 3'ss of exon 5
gtaatttgcctggaaaacaaaatttcacacacatgtactaagatctttaaattttacataatatga--aatgtaatg-taagtatctaacatacaaatccatgtgtagGTTTTGATGGGGTTGAGATCCACGGTGCTCATGGCTACTTACTTGAGCAATTCATTAAAGACAAAGTGAATGATCGAAGTGATGGATATGGTGGATCCCT
| ||| | || | ||| | | | ||| || || ||| | ||| | || | | || | |||| | || ||||||||||||| ||||||||||| || ||||||||||| ||||||| || ||| | | | || || || | || | | | | |
------------gtaaattcatcctctgataca---aatcatggcttagctttctagtcaatttcttcgatgcactgatgataatattgtttaca---caatacatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGGTCAATGATCGAACAGACAAGTATGGTAGATCACTAGAGAACCGTTGCAG
upper sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ28624 (Selaginella moellendorffii), 3'ss of exon 4
gtaatttgcctggaaaacaaaatttcacacacatgtactaagatctttaaattttacataatatgaaatgtaatgtaagtatctaacatacaaatccatgtgtagGTTTTGATGGGGTTGAGATCCACGGTGCTCATGGCTACTTACTTGAGCAATTCATTAAAGACAAAGTGAATGATCGAAGTGATGGATATGGTGGATCCCT
||||| | | | | | | || | | | ||||| | || | ||||||| |||||||| |||||||||||||| ||||| ||||| | | || |||||| | ||||| || || ||| ||| |||| || ||||| || ||
-------------------------------------------gtgttaaactatgctt--ctttctttctagtttcacaggctaacgaa--aaactgggtgtagGCTTTGATGGTGTTGAGATCCACGGGGCTCACGGCTATCTGATCGACCAATTCCTGAAAGATGGTGTCAACGATAGAACGGATGAGTACGGTGGTTCTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttacataatatgaaatgtaatgtaagtatctaacatacaaatccatgtgtagGTTTTGATGGGGTTGAGATCCACGGTGCTCATGGCTACTTACTTGAGCAATTCATTAAAGACAAAGTGAATGATCGAAGTGATGGATATGGTGGATCCCT
atctaac putative branch site (score: 2)
ataatatgaaatgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttgcctggaaaacaaaatttcacacacatgtactaagatctttaaattttacataatatgaaatgtaatgtaagtatctaacatacaaatccatgtgtagGTTTTGATGGGGTTGAGATCCACGGTGCTCATGGCTACTTACTTGAGCAATTCATTAAAGACAAAGTGAATGATCGAAGTGATGGATATGGTGGATCCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA