Sequence
atgc intronic sequence ATGC exonic sequence...aatcaaatttgctcatggccatcatgatatatctttgacaacctgtatattcttctgcttgatgatgttgaaaaataatattaagttctttgatttgcagGAATCTAAATCTCTTAAAAACATACCAGTTGTGATTATGTCCTCAGAGAATGTACCATCAAGGATCAACAG
Basic information
species | Glycine max |
transcript | GLYMA13G26770.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G26770.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g72330.1 (Oryza sativa), 3'ss of exon 3
----aatcaaatttgctcatggccatcatgatatatctttgacaacctgtatattcttctgcttgatgatgttgaaa----aataatattaagttctttgatt--------------tgcagGAATCTAAATCTCTTAAAAACATACCAGTTGTGATTATGTCCTCAGAGAATGTACCATCAAGGATCAACAG
| ||||| | | ||| || ||| | || || | | | || || || || | ||| ||| | |||| | | |||| ||| || | || |||||||||||||||| ||||| || |||||||| || |||||||||||||
gtaagtttttgtttgcagagaattgaattcttat-cctctgagcattcataaatcttgggtccttttgttgctggaagtggagtaaaatttgttccttttgctgttcattttgggggtacagGGATCATCTTCATTGAAGGACATACCAGTTGTGATCATGTCTTCTGAGAATGTGCCTGCAAGGATCAACAG
upper sequence: GLYMA13G26770.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g03430.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------aatcaaatttgctcatggccatcatg-atatatctttgacaacct-gtatattcttctgcttga----------------tgatgttgaa---aaat--aatattaagttcttt--gatttgcagGAATCTAAATCTCTTAAAAACATACCAGTTGTGATTATGTCCTCAGAGAATGTACCATCAAGGATCAACAG
| | || ||||||| || ||| | || | ||| ||| | ||| ||| ||| ||| || ||||| ||| || ||| ||| | || ||||||| |||| |||||| ||| |||||||||||||||| |||||||| ||||| | || |||||||| |||||
gtaagatctctcattttgatcttagctttcaaatttctttgatcttgcagctttctcatggacaacatccagatcagtgtgaaaacttcatattttccactgattgggacttgggaaagttaccaattttgaagccaaactgaagtctaaattcatgtgaatctgcagGAGTCTACATCTCTGAAAGACATACCAGTTGTGATCATGTCCTCTGAGAACATCCCTTCAAGGATTAACAG
upper sequence: GLYMA13G26770.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g03450.t01 (Vitis vinifera), 3'ss of exon 2
aatcaaatttgctcatggccatcatgatatatctttgacaacctgtatattcttctgcttgatgatgttgaaaaataata-----ttaagtt--ctttgatttgcagGAATCTAAATCTCTTAAAAACATACCAGTTGTGATTATGTCCTCAGAGAATGTACCATCAAGGATCAACAG
| | |||| | | || || | || ||| | | | |||| | || | | | | | | | || |||| || | | || ||||||| |||| |||||||||| |||| ||||||||||| |||||||| |||||| | || || ||||| |||||
------gtatcttcatttgcctaattattgaatttcaacatcttat-tattttactccaagttagtcagaacagttcattaaaatttaaattaacatgaatctgcagGAGTCTACATCTCTTAAAGACATCCCAGTTGTGATCATGTCCTCTGAGAATATCCCTTCTAGGATTAACAG
upper sequence: GLYMA13G26770.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g03490.t01 (Vitis vinifera), 3'ss of exon 4
--aatcaaatttgctcatggccatcatgatatatctttgacaacctgtatattcttctgcttgatgatgttgaaaaataatattaagttctttgatt-tgcagGAATCTAAATCTCTTAAAAACATACCAGTTGTGATTATGTCCTCAGAGAATGTACCATCAAGGATCAACAG
| |||||| || | | | | | | | | | || | | || | | | || | ||| | || | ||||| ||||||| ||| |||||| ||| |||||||||||||||| |||||||| ||||| | || |||||||| |||||
gtatcttcatttgccca--attgttacatttcagatcttatt-cttccattccaatttactc-agaacaattaatgaaaatctaaatgaatgtgattctgcagGAGTCTTCATCTCTGAAAGACATACCAGTTGTGATCATGTCCTCTGAGAACATCCCTTCAAGGATTAACAG
upper sequence: GLYMA13G26770.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g03480.t01 (Vitis vinifera), 3'ss of exon 2
aatcaaatttgctcatggccatcatgatatatctttgacaacctgtatattcttctgcttgatgatgttgaaaaataatattaagttct---ttgatttgcagGAATCTAAATCTCTTAAAAACATACCAGTTGTGATTATGTCCTCAGAGAATGTACCATCAAGGATCAACAG
|| | | || ||| | || || || || | | | | || | | | | | | || |||| | | ||| | || ||||||| |||| |||||||||| |||| ||||||||||| |||||||| |||||| | || || ||||| | |||
----gtatcttcatttgcccaat-tattacat-ttcagcatcttatttttttcacgccaagttagtcccaacaattaat-tagaattcaaaatgaatctgcagGAGTCTACATCTCTTAAAGACATCCCAGTTGTGATCATGTCCTCTGAGAATATCCCTTCTAGGATTACCAG
upper sequence: GLYMA13G26770.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g03510.t01 (Vitis vinifera), 3'ss of exon 3
aatcaaatttgctcatggccatcatgatatatctttgacaacctgtatattcttctgcttgatgatgttgaaaaataatattaagttctttgatttgcagGAATCTAAATCTCTTAAAAACATACCAGTTGTGATTATGTCCTCAGAGAATGTACCATCAAGGATCAACAG
||| | || || || || | || | ||| | | ||| || || || | || ||||||||||| |||||| ||| |||||||||||||||| |||||||| |||||| | || |||||||| |||||
------------------gtatcttcattctcctgatgaaaactcagaaccatttt------tgaagctaaaactaaaaatcaaatgaatt---ctgcagGAATCTTCATCTCTGAAAGACATACCAGTTGTGATCATGTCCTCTGAGAATATCCCCTCAAGGATTAACAG
upper sequence: GLYMA13G26770.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g03460.t01 (Vitis vinifera), 3'ss of exon 3
--aatcaaatttgctca-tggcc--atcatgatatatctttgacaacctgtatattcttctgcttgatgatgttgaaaaataatattaagtt--ctttgatttgcagGAATCTAAATCTCTTAAAAACATACCAGTTGTGATTATGTCCTCAGAGAATGTACCATCAAGGATCAACAG
| |||||| | | || | || | || || | || || | | || ||| ||| |||| | | | || ||||||| |||| |||||||||| ||| ||||||||||| |||||||| |||||| | || || ||||| |||||
gtatcttcatttgcctaattattgaatttcaacatcttattattttactccaagttagtcagaacagtt-cattaaaattaaattttaaataaacatgaatctgcagGAGTCTACATCTCTTAAAGGCATCCCAGTTGTGATCATGTCCTCTGAGAATATCCCTTCTAGGATTAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatattcttctgcttgatgatgttgaaaaataatattaagttctttgatttgcagGAATCTAAATCTCTTAAAAACATACCAGTTGTGATTATGTCCTCAGAGAATGTACCATCAAGGATCAACAG
ctttgat putative branch site (score: 5)
ttcttt CT-rich tract
ttgaaaaataatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatcaaatttgctcatggccatcatgatatatctttgacaacctgtatattcttctgcttgatgatgttgaaaaataatattaagttctttgatttgcagGAATCTAAATCTCTTAAAAACATACCAGTTGTGATTATGTCCTCAGAGAATGTACCATCAAGGATCAACAG
- - - - - -ctcatgg
- - - - - - - - - ccatcat
- - - - - - - - - - - - - - - - - - - - acctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa