Sequence
atgc intronic sequence ATGC exonic sequencegtgtttgaaagagaagataagcacacttggatatgatatgcaccatgaaggatggggctttcatgtgaatttcttctgttttggggatgttttcagGCTGGATATTGTTGCAGTAGACAGTCCTATTGGACGTTTGGGCCTCAGTGTTTGCTATGATTTGAGATTTCCAGAGATGTACCAATTGCTACGTTTCCAA
Basic information
species | Glycine max |
transcript | GLYMA20G38690.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38690.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g31830.1 (Oryza sativa), 3'ss of exon 4
----gtgtttgaaagag-aagataagcacacttggatatgatatgcacca---tgaag--gatggggctttcatgtgaatttcttctgttttggggatgttttcagGCTGGA-TATTGTTGCAGTAGACAGTCCTATTGGACGTTTGGGCCTCAGTGTTTGCTATGATTTGAGATTTCCAGAGATGTACCAATTGCTACGTTTCCAA
| | | | | || | | | | | || || | | || || ||| ||| | |||||| | | | ||| || ||||| | | | |||||||| || |||||| ||||||| | || || | |||||||||||||||||||||||||||| | ||||||| | || || |
gattgaaactaatactgcaatagtgatatcatggagtgagacatacgtcgggttgcagttgataacgctat-atgtgatggtgtatttatttat-----ttatcagGTGATACTGTCGTTGCAGTGGATAGTCCTTTTGGACGACTTGGGCTTACTGTTTGCTATGATTTGAGATTTCCAGAGCTTTACCAATGTTTGCGCTTTAA-
upper sequence: GLYMA20G38690.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G145578_T01 (Zea mays), 3'ss of exon 4
----gtgtttgaaagagaagataagcacacttggatatgatat-gcaccatgaaggatggggctttcatgtgaatttcttctgttttggggatgttttcagGCTGGA-TATTGTTGCAGTAGACAGTCCTATTGGACGTTTGGGCCTCAGTGTTTGCTATGATTTGAGATTTCCAGAGATGTACCAATTGCTACGTTTCCAA
||| | | | || || || | | |||| | | | ||| | || || | |||||| | || ||||| | ||||||||| || || || ||| ||||||| ||||| || | ||||||||||||||||||||| |||||| | || ||| | | ||||| |
aatagtggtgtcttggatgaagtagtactgctgt-tgtaatattgaattgcaattgattccatatatgtgattgcttatgatgttttctctctcttatcagGTGATACTATTGTTGCTGTGGATAGCCCTTTTGGACGGTTGGGGCTTACTGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAA-
upper sequence: GLYMA20G38690.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0067g03530.t01 (Vitis vinifera), 3'ss of exon 4
--------gtgtttgaaagagaagataagcacacttggatatgatatgcaccatgaaggatggggctttcatgtgaatttc--ttctgttttggggatgttttcagGCT-GGATATTGTTGCAGTAGACAGTCCTATTGGACGTTTGGGCCTCAGTGTTTGCTATGATTTGAGATTTCCAGAGATGTACCAATTGCTACGTTTCCAA
|||||| | || || | | || || || ||| | ||| | |||| |||| | |||| |||| || ||||||||| ||| ||||||| |||||||| || ||||| |||||||| | | |||||||||||||||||||| |||||| | || || |||| | ||||
tttttctggtgtttcccaagtaa--tagttgccttatgacataattga----atggatgatttgacttttttgtgtgtgagaattctaaattggtgaagttttcagGGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAGCAGCTAAGGTTCCT- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accatgaaggatggggctttcatgtgaatttcttctgttttggggatgttttcagGCTGGATATTGTTGCAGTAGACAGTCCTATTGGACGTTTGGGCCTCAGTGTTTGCTATGATTTGAGATTTCCAGAGATGTACCAATTGCTACGTTTCCAA
tgttttc CT-rich tract
aatttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtttgaaagagaagataagcacacttggatatgatatgcaccatgaaggatggggctttcatgtgaatttcttctgttttggggatgttttcagGCTGGATATTGTTGCAGTAGACAGTCCTATTGGACGTTTGGGCCTCAGTGTTTGCTATGATTTGAGATTTCCAGAGATGTACCAATTGCTACGTTTCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG