Sequence
atgc intronic sequence ATGC exonic sequence...ttctaaaattgagtgactattgtggttctattaatgaaaattttaagtgtaatgtgtaataaattcaaaaggcaccttgcttatatgtatgattttgcagATACCAGAACTGGATTTTGAGATTCCACCAGAAGCTCAACGTGGTAGTCTGTCAACG
Basic information
species | Glycine max |
transcript | GLYMA20G02690.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G02690.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g36774.1 (Oryza sativa), 3'ss of exon 5
ttctaaaattgagtgactattgtggttctattaatgaaaattttaagtgtaatgtgtaataaattcaaaaggcaccttgcttatatgtatgattttgcagATACCAGAACTGGATTTTGAGATTCCACCAGAAGCTCAACGTGGTAGTCTGTCAACG
| || | | | ||| | ||| |||||| | || |||||| | | | | | ||| | | ||| | | |||| ||||||||||| |||||||| || ||||||||||||||||| || |||||
----------gtatgtcaaactatgctcttgtgatgct--ttttaaatata---tgtaatgtgatttatatgtaactt-----cacatttgacgt-gtagATTCCAGAACTGGACTTTGAGATCCCTCCAGAAGCTCAACGTGGATCACTTTCAACA
upper sequence: GLYMA20G02690.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G351582_T01 (Zea mays), 3'ss of exon 6
---ttctaaaattgagtgactattgtggttc-tattaatgaaaattttaagtgtaatgtgtaataaattcaaaaggcaccttgcttatatgtatgattttgcagATACCAGAACTGGATTTTGAGATTCCACCAGAAGCTCAACGTGGTAGTCTGTCAACG
| || | ||| ||| || || | | | | | || | || | || | || | ||| || | | || |||| | ||||||| ||||| || || |||||||| || ||||||||||||||||| | || || ||
gtatgctgatatt---tgatcatcttgatacatcacagtaaatacattgaatgcattgctt------ttctaa-------ctattcat-tgtacccatctgcagATTCCAGAGCTCGACTTTGAGATCCCTCCAGAAGCTCAACGTGGAACACTTTCTACT
upper sequence: GLYMA20G02690.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G37340.3 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------------------------------------------------------------------ttctaaaattgagtgactattgtggttctattaatgaaaattttaagtgtaatgtgtaa-taaattcaaaaggcaccttgcttatatgtatgattttgcagATACCAGAACTGGATTTTGAGATTCCACCAGAAGCTCAACGTGGTAGTCTGTCAACG
|| ||| | || | | |||| |||| || | | || || | | | | | | | |||| | || |||| || ||||| || |||||||||||||||||||||||||| || ||| |||||||| | || |||
gtgagttctcttactgattctgggaaattcaatgcatcttcggattcagtattttcttaaccgagcatatttataagaaacagcttcccctaatctccctgaaaactgtgaattagtttccttcttataatatgaaaactggac-tgatttgaagctggaaactgatagtagtttgcattaatatatgtatt--cagATTCCTGAACTGGATTTTGAGATTCCACCAGAGGCCCAAAGTGGTAGTTTATCTACG
upper sequence: GLYMA20G02690.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G22480.1 (Arabidopsis thaliana), 3'ss of exon 6
-----ttctaaaattgagtgactattgtggttctatta--atgaaaattttaagtgtaatgtgtaa-taaattcaaaaggcaccttgcttatatgtatgattttgcagATACCAGAACTGGATTTTGAGATTCCACCAGAAGCTCAACGTGGTAGTCTGTCAACG
|| |||| || | | || | || || | || ||||||| | | | || || | | | | | | | |||| ||| | || | ||||| || |||||||||||||||||||||||||| || |||||||| ||| |||| ||
acgtttttgaaaactgtg-aattagtttgcttatcataccatgaaaact---ggactgatttgaagctggaaactgacagtagtttgcgaataaat----ttcttcagATTCCTGAACTGGATTTTGAGATTCCACCAGAGGCCCAACGTGGAAGTTTGTCTACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgtaatgtgtaataaattcaaaaggcaccttgcttatatgtatgattttgcagATACCAGAACTGGATTTTGAGATTCCACCAGAAGCTCAACGTGGTAGTCTGTCAACG
tgtaataaattcaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctaaaattgagtgactattgtggttctattaatgaaaattttaagtgtaatgtgtaataaattcaaaaggcaccttgcttatatgtatgattttgcagATACCAGAACTGGATTTTGAGATTCCACCAGAAGCTCAACGTGGTAGTCTGTCAACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - -tgagtga
- - - - - - - - - - tgtggtt