Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaacaaacatcacttcattgtgcattaagttttactttgaactttccttcttgacctattatgtgtgcaactatatataatgattcatgatttgtaatatttagGTTGATTTGGAGCATAATCAATATCGCACTTTCCAAGGCTTGACTTGCCTGATGCAAATCTCAACAAGGACTGAAGATTTTATTGTTGACACTTTGAAAC
Basic information
species | Glycine max |
transcript | GLYMA05G13920.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 2
gtaaaaacaaacatcacttcattgtgcattaagttttactttgaactttccttcttgac-ctattatgtgtgcaactatatataatgattcatgatttgtaatatttagGTTGATTTGGAGCATAATCAATATCGCACTTTCCAAGGCTTGACTTGCCTGATGCAAATCTCAACAAGGACTGAAGATTTTATTGTTGACACTTTGAAAC
| | | | | |||| || | | | | |||| ||| ||| | | | | | || || | | || || |||| ||| ||||||||||||||||| | | || || |||||||| ||| ||||||| || |||||||| || ||||| |||||||| |||||| | || |
---atgttctaggctatctgac-atgcaatagaataaattcca---tggacttcatgatactagcaatttaatgattgcctctataatttttttgctcc--attttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
upper sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G145704_T02 (Zea mays), 3'ss of exon 2
gtaaaaacaaacatcacttcattgtgcattaagttttactttgaactttccttcttgac-ctattatgtgtgcaactatatataatgattcatgatttgtaatatttagGTTGATTTGGAGCATAATCAATATCGCACTTTCCAAGGCTTGACTTGCCTGATGCAAATCTCAACAAGGACTGAAGATTTTATTGTTGACACTTTGAAAC
| | | | | |||| || | | | | |||| ||| ||| | | | | | || || | | || || |||| ||| | ||||||||||||||| | | || || |||||||| ||| ||||||| || |||||||| || ||||| |||||||| |||||| | || |
---atgttctaggctatctgac-atgcaatagaataaattcca---tggacttcatgatactagcaatttaatgattgcctctataatttttttgctcc--attttcagGTAGATCTAGAGCATAATCAATATAGGTCATTTCAGGGCTTGACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
upper sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G039096_T01 (Zea mays), 3'ss of exon 3
gtaaaaacaaacatcacttcattgtgcattaagttttactttgaactttccttcttgac-ctattatgtgtgcaactatatataatgattcatgatttgtaatatttagGTTGATTTGGAGCATAATCAATATCGCACTTTCCAAGGCTTGACTTGCCTGATGCAAATCTCAACAAGGACTGAAGATTTTATTGTTGACACTTTGAAAC
| | | | | |||| || | | | | |||| ||| ||| | | | | | || || | | || || |||| ||| ||||||||||||||||| | | || || ||||| || ||| ||||||| || |||||||| || ||||| |||||||| |||||| | || |
---atgttctaggctatctgac-atgcaatagaataaattcca---tggacttcatgatactagcaatttaatgattgcctctataatttttttgctcc--attttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTCACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
upper sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G452875_T01 (Zea mays), 3'ss of exon 2
gtaaaaacaaacatcacttcattgtgcattaagttttactttgaactttccttcttgac-ctattatgtgtgcaactatatataatgattcatgatttgtaatatttagGTTGATTTGGAGCATAATCAATATCGCACTTTCCAAGGCTTGACTTGCCTGATGCAAATCTCAACAAGGACTGAAGATTTTATTGTTGACACTTTGAAAC
| | | || | |||| || | | | | |||| ||| ||| | | | | | || || | | || || |||| ||| ||||||||||||||||| | | || || ||||||| ||| ||||||| || |||||||| || ||||| |||||||| |||||| | || |
---atgttctaggctatttgac-atgcaatagaataaattcca---tggacttcatgatactagcaatttaatgattgcctctataatttttttgctcc--attttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTGATCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
upper sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 2
gtaaaaacaaacatcacttcatt-gtgcattaagttttactttgaactttccttcttgacc-tattatgtgtgcaactatatataatgattcatgatttgtaatattt----agGTTGATTTGGAGCATAATCAATATCGCACTTTCCAAGGCTTGACTTGCCTGATGCAAATCTCAACAAGGACTGAAGATTTTATTGTTGACACTTTGAAAC
|||| ||| || ||| | | | |||||||| || | ||| ||| | | | | | || || || || | || |||| ||| ||||||||||||| ||| | ||||| ||||| || || ||| ||||||||||||| || || || || |||| ||||||||| | || || |
--------------aacttaatttatgagttaggatgatggtatctctttccttatttattatatcttgtttatcgttcttgcttgagtttgttgtcttttattccttttgtagGTCGATCTGGAGCATAATCAGTATAGAACTTTTCAAGGATTAACATGCTTGATGCAAATCTCTACTAGAACCGAGGATTATATTGTTGATATATTCAAGC
upper sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaaaacaaacatcacttcattgtgcattaagttttactttgaactttccttcttgacctattatgtgtgcaactatatataatgattcatgatttgtaatatttagGTTGATTTGGAGCATAATCAATATCGCACTTTCCAAGGCTTGACTTGCCTGATGCAAATCTCAACAAGGACTGAAGATTTTATTGTTGACACTTTGAAAC
| | | || | || || || || || ||| | | |||| | | | | ||| || |||| | ||||||||||| ||||||||||||| ||| | |||| ||||| ||||| ||| |||||||||| || || || || || |||| ||| ||||| || || || |
-------ctctccttgattagataagc-caaaaaaatatattcaagtttgagttgccaatgcttatttctcccctttctcttaagttttttgtttttgctctttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC
upper sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0056g01320.t01 (Vitis vinifera), 3'ss of exon 1
--gtaaaaacaaacatcacttcattgtgcattaagttttactttgaactttccttcttgacctattatgtgtgcaactatatataatgattcatgatttgtaatatttagGTTGATTTGGAGCATAATCAATATCGCACTTTCCAAGGCTTGACTTGCCTGATGCAAATCTCAACAAGGACTGAAGATTTTATTGTTGACACTTTGAAAC
| | | |||| | | ||||| | | || | | | | ||| ||| || | | || | | | | || ||| | | | | ||||||||| |||| |||||||| ||||| |||| ||||| ||||||||| ||||||||||||| || |||||||| |||||| ||||||| || | || |
ctatcacttctaacaagaaatttacgtgca---aataatatgtacataatgtcatctggactagcta-attttcaggtctct----ttctttttgaactat--tgtctagGTTGATCTGGAACATAATCAGTATCGATCTTTTCAAGGGTTGACTTGCTTGATGCAAATCTCTACTAGGACTGAGGATTTTGTTGTTGATACACTAAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgacctattatgtgtgcaactatatataatgattcatgatttgtaatatttagGTTGATTTGGAGCATAATCAATATCGCACTTTCCAAGGCTTGACTTGCCTGATGCAAATCTCAACAAGGACTGAAGATTTTATTGTTGACACTTTGAAAC
tcttgac putative branch site (score: 3)
aactatatataatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaacaaacatcacttcattgtgcattaagttttactttgaactttccttcttgacctattatgtgtgcaactatatataatgattcatgatttgtaatatttagGTTGATTTGGAGCATAATCAATATCGCACTTTCCAAGGCTTGACTTGCCTGATGCAAATCTCAACAAGGACTGAAGATTTTATTGTTGACACTTTGAAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA