Sequence
atgc intronic sequence ATGC exonic sequence...ttggatttacccattgcctatccctacaatcattgatgttaccggtaaacagatctagttttgcttctgatgtgtacctcactaattactatttttatagGGTGGGATATACACTCTTCCTAGTCATCTATCACCTGGTGCTAGAGATTTGATACCAAGGATGCTTGTGGTGGATCCCATGAAGAGGATGACCATACCTG
Basic information
species | Glycine max |
transcript | GLYMA13G05700.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 5
ttggatttacccattgcctatccctacaatcattgatgttaccggtaaacagatctagttttgc-ttctgatgtgtacctcactaattactatttttatagGGTGGGATATACACTCTTCCTAGTCATCTATCACCTGGTGCTAGAGATTTGATACCAAGGATGCTTGTGGTGGATCCCATGAAGAGGATGACCATACCTG
| | | ||||| ||| | | || | || |||| |||| | | | || | ||| | | | | || |||||||| ||||| || ||||| |||||| | |||||| || || |||||||| || || |||||||| || ||||||||||||||||| ||||||| ||
gttagcaaagatgtgatatatcc-tactgataaaggtgctgcctc-------atctccttttatatgttaaagtaaaactctgtccgttttgatgttctagGGTGGCATATATACCCTTCCCAGTCATTTGTCACCTTTGGCAAGGGATTTGATTCCCAGAATGCTTGTTGTTGATCCCATGAAGAGGATCACCATACGTG
upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 5
-----ttggatttaccca---ttgcctatccctacaatcattgatgtt-accgg-------taaacagatcta-gttttgcttctgat---gtgtacctcactaatta--ctattt--------ttatagGGTGGGATATACACTCTTCCTAGTCATCTATCACCTGGTGCTAGAGATTTGATACCAAGGATGCTTGTGGTGGATCCCATGAAGAGGATGACCATACCTG
| |||||| | | ||| || | || | | ||||| || | | || | ||||| ||||| || | || || || | | || || || ||| || ||||||| ||||| ||||| || |||||| |||| || || ||||||||||| |||||||||||||| || ||||| |||||||| || || || | ||
gtgagatagatttatgtaggctagccagaccttgtaaactcttatgttgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGAGATTTGATCCCAAGGATGCTTGTTGTTGATCCAATGAAGAGAATCACAATTCGTG
upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 3'ss of exon 5
-----ttggatttaccca---ttgcctatccctacaatcattgatgtt-accgg-------taaacagatcta-gttttgcttctgat---gtgtacctcactaatta------ctattt----ttatagGGTGGGATATACACTCTTCCTAGTCATCTATCACCTGGTGCTAGAGATTTGATACCAAGGATGCTTGTGGTGGATCCCATGAAGAGGATGACCATACCTG
| ||||| | | || || || || | | ||| | || | | || | ||||| ||||| || | || || || | | || || | ||| || ||||||| ||||| ||||| || |||||| |||| || || || |||||||| |||||||||||||| || ||||| |||||||| || || || | ||
gtgagataaatttatgtaggctaaccagaccttataaactcttatgctgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgcttgtttggtgttccagGGTGGTATATATACTCTCCCAAGTCATTTATCTGCTCTGGCCAGGGATTTGATCCCAAGGATGCTTGTTGTTGATCCAATGAAGAGAATCACAATTCGTG
upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 5
----------ttggatttacccatt-gcctatccctac-aatcattgatgttaccggtaaacagatctagttttgcttctgatgtgtacctcactaattactatttt-----tatagGGTGGGATATACACTCTTCCTAGTCATCTATCACCTGGTGCTAGAGATTTGATACCAAGGATGCTTGTGGTGGATCCCATGAAGAGGATGACCATACCTG
|| | | | || | |||| || ||| |||| || | | || | |||| ||| |||| | || || |||| ||||||| ||||||||||| | ||||| ||| |||| |||||||||||||||||||| || |||||||||| || || |||||||| | | ||||| ||||
gtacattctattactcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgactgta-accttttttttttctcttttcgtcctatagGGAGGGATATACACATTACCTAGCCATTTATCTCCTGGTGCTAGAGATTTGATCCCCCGGATGCTTGTAGTTGACCCCATGAAACGAGTAACCATCCCTG
upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 5
ttggatttacccattgcctatccctacaatcattgatgttaccggtaaacagatctagttttgcttctgatgtg---tacctcactaattactatttttatagGGTGGGATATACACTCTTCCTAGTCATCTATCACCTGGTGCTAGAGATTTGATACCAAGGATGCTTGTGGTGGATCCCATGAAGAGGATGACCATACCTG
| | | || | | || | | | |||| ||| | | || | ||| || || | | || | | | | ||||||||||| ||||||||||| |||||| ||||| ||| |||||||| |||| |||||||||||| | || || || |||| | || ||||| ||||
---gtactgtacgttatactttgattcagctaa-aagactcttcttaaatggattca--tatgtatgtgaagtaacttatcaaggtgttttttttctctttagGGTGGGATTTACACTCTTCCAAGTCATTTATCATCTGAGGCTAGAGACCTGATCCCAAGGATGCTTATAGTTGACCCGGTGAAACGAATCACCATTCCTG
upper sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 5
---ttggatttacccattgcctatccc-tacaatcattgatgttaccggtaaacagatctagttttgcttctgatgtgtacctcactaattactatttttatagGGTGGGATATACACTCTTCCTAGTCATCTATCACCTGGTGCTAGAGATTTGATACCAAGGATGCTTGTGGTGGATCCCATGAAGAGGATGACCATACCTG
| || | | || | | |||| | || | | | || || || | ||| | ||| |||||| ||||||||||||| ||||||||||||||| ||||| |||||||||||||| |||| ||||||||||| | || || || |||||| | ||||| || ||||
gctcttatcctataaagagtacattttatcctatcaatcatat-attattttctgagattaaaaatgtttgctccataaacccatttcatttgtatttt---agGGTGGGATATATACTCTTCCTAGTCATTTATCAACTGGTGCTAGAGATCTGATCCCAAGGATGCTCATAGTTGACCCTATGAAGCGAATGACAATTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaacagatctagttttgcttctgatgtgtacctcactaattactatttttatagGGTGGGATATACACTCTTCCTAGTCATCTATCACCTGGTGCTAGAGATTTGATACCAAGGATGCTTGTGGTGGATCCCATGAAGAGGATGACCATACCTG
cactaat putative branch site (score: 2)
ctattttt putative PPT
tcactaattactattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttggatttacccattgcctatccctacaatcattgatgttaccggtaaacagatctagttttgcttctgatgtgtacctcactaattactatttttatagGGTGGGATATACACTCTTCCTAGTCATCTATCACCTGGTGCTAGAGATTTGATACCAAGGATGCTTGTGGTGGATCCCATGAAGAGGATGACCATACCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG