Sequence
atgc intronic sequence ATGC exonic sequence...aataatcttattgcaatctcaaaatacaatcttatcatgatatcaattattcatttaatctgtgtttgaatcagattcttaccttgtgtatgattgttagGAAGAAGTTATCCAATCAGGTGGTCAGATTGAGCCGCCTGGAATGCACATGATTTATCTTCCATATTCTGATGACATCAGATTTGTTGAAGAG
Basic information
species | Glycine max |
transcript | GLYMA20G39280.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G39280.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os07g08729.1 (Oryza sativa), 3'ss of exon 14
aataatcttattgcaatct--caaaatacaatcttatcatgatatcaattattcatttaatctgtgtttgaatca-gattcttaccttgtgtatgattgttagGAAGAAGTTATCCAATCAGGTGGTCAGATTGAGCCGCCTGGAATGCACATGATTTATCTTCCATATTCTGATGACATCAGATTTGTTGAAGAG
|| | ||| | ||| | ||| | | ||| |||| | || | | | | || | || || | | | ||||||| |||| | |||||||| ||||| || |||||||| |||||||| ||||||||||| || ||||| | |||| | ||| |||
---tttcgttttgtattctgtctgaattttgtttgtcagggattcttattacatagctatatcttatatactttttgaaattgactctggagaaaaataacagGAAGAGGTTACTTCTGCTGGTGGTCAAATTGAACCACCTGGAATACACATGATCTATCTTCCATACTCGGATGATGTTAGATATCCTGAGGAG
upper sequence: GLYMA20G39280.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G414496_T05 (Zea mays), 3'ss of exon 14
---aataatcttattgcaatctcaaaatacaatcttatcatgatatcaat-tattcatt-taatctg-tgtttgaatcagattcttaccttgtgtatgattgttagGAAGAAGTTATCCAATCAGGTGGTCAGATTGAGCCGCCTGGAATGCACATGATTTATCTTCCATATTCTGATGACATCAGATTTGTTGAAGAG
| || | | | | || || || |||||||| | ||| || ||| || | || || | ||| || || || ||||||| |||| || ||| ||||| |||| |||||||| ||||||||||| ||||||||||| || ||||| || |||| | ||||||
gtgagggattgtgtcctaccatgtttatttaac---attttgatatcagtatatatatcctaacatgcttttcaaaatcaactctggtctattggtcaataa--agGAAGAGGTTACTTCGTCTGGTCGTCAGTTTGAACCGCCTGGCATGCACATGATCTATCTTCCATACTCCGATGATATTAGATATCCTGAAGAA
upper sequence: GLYMA20G39280.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G414496_T08 (Zea mays), 3'ss of exon 13
---aataatcttattgcaatctcaaaatacaatcttatcatgatatcaat-tattcatt-taatctg-tgtttgaatcagattcttaccttgtgtatgattgttagGAAGAAGTTATCCAATCAGGTGGTCAGATTGAGCCGCCTGGAATGCACATGATTTATCTTCCATATTCTGATGACATCAGATTTGTTGAAGAG-------
| || | | | | || || || |||||||| | ||| || ||| || | || || | ||| || || || ||||||| |||| || ||| ||||| |||| |||||||| ||||||||||| ||||||||||| || ||||| || |||| | ||||||
gtgagggattgtgtcctaccatgtttatttaac---attttgatatcagtatatatatcctaacatgcttttcaaaatcaactctggtctattggtcaataa--agGAAGAGGTTACTTCGTCTGGTCGTCAGTTTGAACCGCCTGGCATGCACATGATCTATCTTCCATACTCCGATGATATTAGATATCCTGAAGAAGTAAGGA
upper sequence: GLYMA20G39280.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv05s0062g01170.t01 (Vitis vinifera), 3'ss of exon 14
--aataatcttattgcaatctcaaaatacaatcttatcatgatatcaattattcatt-taatctgtgtttg-aatcagattcttaccttgtgtatgattgttagGAAGAAGTTATCCAATCAGGTGGTCAGATTGAGCCGCCTGGAATGCACATGATTTATCTTCCATATTCTGATGACATCAGATTTGTTGAAGAG
| | || | | ||| || | | | || | || | |||||| || | | || || || | | ||| | ||| | | || |||| || | || |||| |||| ||||||| || || ||||| ||||| |||||||||||||||||||| |||||| | ||||||
ctgaaagtccgagtaaaattgtaattgttattttcatgtttcta--agttattctttacattttgcacttatgataaaactctaattttg-atgaaactgc-agGATGAGATCATTGCTGGTGGTGTTCAGGTTGAGCCACCAGGCATGCATATGATATATCTTCCATATTCTGATGATATCAGACACATCGAAGAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|18041148|gb|BM309442.1|BM309442EST: CATTTAGTGGTAGTTCCTCTCGCCCTCAATTGGTTGCTCTTATTGCGCAG GAAGAAGTTATCCAATCAGGTGGTCAGATTGAGCCGCCTGGAATGCACATG
genomic: CATTTAGTGGTAGTTCCTCTCGCCCTCAATTGGTTGCTCTTATTGCGCAGgtacaatatg ... tgattgttagGAAGAAGTTATCCAATCAGGTGGTCAGATTGAGCCGCCTGGAATGCACATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attattcatttaatctgtgtttgaatcagattcttaccttgtgtatgattgttagGAAGAAGTTATCCAATCAGGTGGTCAGATTGAGCCGCCTGGAATGCACATGATTTATCTTCCATATTCTGATGACATCAGATTTGTTGAAGAG
ttcttac putative branch site (score: 2)
tcatttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aataatcttattgcaatctcaaaatacaatcttatcatgatatcaattattcatttaatctgtgtttgaatcagattcttaccttgtgtatgattgttagGAAGAAGTTATCCAATCAGGTGGTCAGATTGAGCCGCCTGGAATGCACATGATTTATCTTCCATATTCTGATGACATCAGATTTGTTGAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - -tgcaatc
- - - - - - - - - - - - - - - - - -catgata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtttg