Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaagactcgatatttaggagcctcaacatcagcataaaattaaagcaaatcaaataacaatgattgctaacacatgtgatataataagtattattgttgctaattatttgtgttcttcaattaatattctgtgtgtttctctaaagGTTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCGACCAACATTCTCTATACTTTTGGTGGGCATGCTGTTACAGT
Basic information
species | Glycine max |
transcript | GLYMA06G11540.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G11540.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
gtaaaaagactcgatatttaggagcctcaacat-cagcataaaattaaagcaaatc-aaataacaa--tgattgctaacacatgtgatataataagtattattgttgctaattatttgtgttcttcaattaatattctgtgtgtttctctaaagGTTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCGACCAACATTCTCTATACTTTTGGTGGGCATGCTGTTACAGT
||| | || | | | | | ||| |||||| | | || |||| | | | ||| |||| | || | | || | || || | ||||||| || ||| || | || |||| || || |||| |||| | || || | || |||| ||||||||||| ||||| || ||||||||||| || || |||||||| |||||||| ||
gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacat-tattacattgcgttgtgctgaaa--aaacacttgtgttttt------------tgtatgaatatc---agGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
upper sequence: GLYMA06G11540.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
gtaaaaagactcgatatttaggagcctcaacatcagcataaaattaaagcaaatcaaataacaatgattgctaacacatgtgatataataagtattattgttgctaattatttgtgttcttcaattaatattctgtgtgtttctctaaagGTTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCGACCAACATTCTCTATACTTTTGGTGGGCATGCTGTTACAGT--
|| ||| || || ||||| | | | || | |||| | | || | | | || ||||| |||| | | ||| |||| | ||||||| || |||| |||| | ||||| |||| |||| ||||||||||| ||||| || ||||||||||| ||||| || ||||| |||||||| ||
---------------------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctg-tgggtg--accggccgagacgatgtgtgtgcttc---tgctgctctacttgttgc-----agGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
upper sequence: GLYMA06G11540.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
gtaaaaagactcgatatttaggagcctcaacatcagcataaaattaaagcaaatcaaataacaatgattgctaacacatgtgatataataagtattattgttgctaattatttgtgttcttcaattaatattctgtgtgtttctctaaagGTTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCGACCAACATTCTCTATACTTTTGGTGGGCATGCTGTTACAGT
|| ||| || || ||||| | | | || | |||| | | || | | | || ||||| |||| | | ||| |||| | ||||||| || |||| |||| | ||||| |||| |||| ||||||||||| ||||| || ||||||||||| ||||| || ||||| |||||||| ||
---------------------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctg-tgggtg--accggccgagacgatgtgtgtgcttc---tgctgctctacttgttgc-----agGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
upper sequence: GLYMA06G11540.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
gtaaaaagactcgatatttaggagcctcaacatcagcataaaattaaagcaaatcaaataacaatgattgctaacacatgtgatataataagtattattgttgctaattatttgtgttcttcaattaat---attctg-tgtgtttctctaaagGTTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCGACCAACATTCTCTATACTTTTGGTGGGCATGCTGTTACAGT
||| || ||| | || ||| | | | | ||| || | ||| | || | | ||| | | ||| || | | | || | || |||| || ||| | || || | | |||||||||||||||| |||| | || ||| ||||| |||||||||||||||||||||| |||||||||||||| || |||||||| |||||||| |||||
-------------gtatgtatttacctta--attagc-tgtattca-------tcacttagttttaatttcaaataattcccata-atcccatcccccctttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT
upper sequence: GLYMA06G11540.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S211_67V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaaaaagactcgatatttaggagcctcaacatcagcataaaattaaagcaaatcaaataacaatgattgctaacacatgtgatataataagtattattgttgctaattatttgtgttcttcaattaatattctgtgtgtttctctaa--agGTTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCGACCAACATTCTCTATACTTTTGGTGGGCATGCTGTTACAGT
| || | | |||| | | ||||| | | | | | | | | | | || | | || | | || ||||| | | | |||||| || || || | ||| | | ||| | |||||||| || || ||||||||||| |||||||| ||||| || |||||||| ||
-----------------------------------gtgacgaactgttcctcttcaa-tggtataaattgcaactggttttcagtcacagaatccttccatcaatt-ttgctctcatactcctaacaaggttctgaactgtgatggagctagGTTGCCAATGTCGTCCATACGGCGCCGACAACGAAGGTCTTGTACTTCACAGGAGCAACCAACATTCTGTATACTTTCGGTGGCCACGCTGTTACTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattgttgctaattatttgtgttcttcaattaatattctgtgtgtttctctaaagGTTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCGACCAACATTCTCTATACTTTTGGTGGGCATGCTGTTACAGT
tgtttctct CT-rich tract
taattatttgtgttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaagactcgatatttaggagcctcaacatcagcataaaattaaagcaaatcaaataacaatgattgctaacacatgtgatataataagtattattgttgctaattatttgtgttcttcaattaatattctgtgtgtttctctaaagGTTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCGACCAACATTCTCTATACTTTTGGTGGGCATGCTGTTACAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT