Sequence
atgc intronic sequence ATGC exonic sequence...ttgggattgttgatccttgaaaacaatcatggtcttttttactataactcctacaagtctgatctaggttttttttttgggtatgttgtgttgtctatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGATCAACAGCGGAGCCAGGCTCTTGAAGCACATGCGGCATCATTTGCTCAATTCAAA
Basic information
species | Glycine max |
transcript | GLYMA18G02960.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 5
ttgggattgttgatccttgaaaacaatcatggtcttttttactataactcctacaagtctgatctaggttttttt--tttgggtatgttgtgttgtctat-----agAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGATCAACAGCGGAGCCAGGCTCTTGAAGCACATGCGGCATCATTTGCTCAATTCAAA
|| | ||| | | || || | | || | || | || |||| | | | | | | || | | || | | ||||||||||| |||| || ||||| |||||||| || ||||||||||| || || || ||||| |||||||| ||||| ||||| ||||| ||| ||
----atatgctacacct---atgctggagcagttcttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 5
ttgggattgttgatccttgaaaacaatcatggtcttttttactataactcctacaagtctgatctaggttttttt--tttgggtatgttgtgttgtctat-----agAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGATCAACAGCGGAGCCAGGCTCTTGAAGCACATGCGGCATCATTTGCTCAATTCAAA
|| | ||| | | | || ||| | | || | || | || |||| | | | | | | || | | || | | ||||||||||| |||| || ||||| |||||||| || ||||||||||| || || || ||||| |||||||| ||||| ||||| ||||| ||| ||
----atatgctacacct---atgctggaacagtttttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 4
ttgggattgttga---tccttgaaaacaatcatggtcttttttactataactcctacaagtctgatctaggttttttttttgggtatgttgtgttgtctatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGATCAACAGCGGAGCCAGGCTCTTGAAGCACATGCGGCATCATTTGCTCAATTCAAA-
|| | || | || || || | || || || ||| | | | || | | ||| | | | || || | |||| |||||| |||| || ||||| |||||||| || ||||| ||||||||||| |||||||| |||||||| ||||| ||||| ||||| ||| ||
-cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgt-tgtatgtgcttctcatatttgtat-gccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAGG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
ttgggattgttga---tccttgaaaacaatcatggtcttttttactataactcctacaagtctgatctaggttttttttttgggtatgttgtgttgtctatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGATCAACAGCGGAGCCAGGCTCTTGAAGCACATGCGGCATCATTTGCTCAATTCAAA
|| | || | || || || | || || || ||| | | | || | | ||| | | | || || | |||| |||||| |||| || ||||| |||||||| || ||||| ||||||||||| |||||||| |||||||| ||||| ||||| ||||| ||| ||
-cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgt-tgtatgtgcttctcatatttgtat-gccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
ttgggattgttgatccttgaaaacaatcatggtctttt-ttactataactcctacaagtctgat-ctaggttttttttttgggtatgttgtgttgtctatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGATCAACAGCGGAGCCAGGCTCTTGAAGCACATGCGGCATCATTTGCTCAATTCAAA
| | || || || | ||| | | | || | ||| || | | | || | ||| | |||| ||| ||||| | ||||||||| |||||||| ||||| || ||||||||||||||||||||||| ||||| ||||| |||||||| ||||| ||||| || || ||
gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttcatgttgtagattcttgactgatcttgtcattattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
ttgggattgttgatccttgaaaacaatcatggtcttttttactataactcctacaagtctgatctaggttttttttttgggtatgttgt----gttgtctatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGATCAACAGCGGAGCCAGGCTCTTGAAGCACATGCGGCATCATTTGCTCAATTCAAA
| || || || || | || | | | || || | | || || | || ||||| ||| | | ||| ||||| ||||||||||| |||||||| ||||| || ||||||||||||||||||||||||||||| |||||||||||||| ||||| |||||||| || ||
gtagggttcctgcaccacg-----tattaggttgaattaagacatcataacggcagtcatgttgtatatttttgacggaatcttgtcattattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 5
ttgggattgttgatccttgaaaacaatcatggtcttttttactataactcctacaagtctgatctaggttttttttttgggtatgttgtgttgtctatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGATCAACAGCGGAGCCAGGCTCTTGAAGCACATGCGGCATCATTTGCTCAATTCAAA
|| | | | | ||| || | | | | | ||| | |||||| |||| |||||||||||||||||||| || || ||||| ||||| || || ||| | ||||| ||||| ||||| || ||| ||||||
--------------------------------------------------gtatccatttcttgaaaagtttcttgtagctaacaaagaaactcttttagCGTCCACAACTGGTGAAAGGAAACATGCAACTCTTTTCAGTCGATCAGCAGCGAAGTCAAGCTTTGGAAGCTCATGCTGCATCTTTCGCTACATTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactcctacaagtctgatctaggttttttttttgggtatgttgtgttgtctatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGATCAACAGCGGAGCCAGGCTCTTGAAGCACATGCGGCATCATTTGCTCAATTCAAA
taggtttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgggattgttgatccttgaaaacaatcatggtcttttttactataactcctacaagtctgatctaggttttttttttgggtatgttgtgttgtctatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGATCAACAGCGGAGCCAGGCTCTTGAAGCACATGCGGCATCATTTGCTCAATTCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- gggattg
- - - - - - - - - -aaaacaa
- - - - - - - - - - - - - -catggtc
- - - - - - - - - - - - - - - - - - - - - - - -ctcctac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtatgt