Sequence
atgc intronic sequence ATGC exonic sequencegtacaaaaccaattgcctggttattggaattgaagtctctacttactgccaaatgatttgtttcctatacacatctatctttatgcttacgattttcgaataattcatagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCTCATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
Basic information
species | Glycine max |
transcript | GLYMA03G42280.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
gtacaaaaccaattgcctggttattggaattgaagtctctacttact-gccaaatgatttgtttcctat--acacatctatctttatgcttacgattttcgaataattcatagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCTCATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
|| ||||| || | |||| | || || | || || ||| | | | || | | || | | || | | | | || | |||| || || || | || ||||||||||| ||||| ||||| |||||||| || || | ||||| |||||||||||||||||||| |||||| |||| |
----------ctgtgttgtattatttgat---aggtctgcatttgtaagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
upper sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 3
gtacaaaaccaattgcctggttattggaattgaagtctctacttactgccaaatgatttgtttcctatacac-atctatctttatgcttacgattttcgaa--taattcatagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCTCATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
|| ||| || || || ||| | | | | | ||| | | | | |||| |||| |||| | | | | ||||||||||||| ||||| || ||||| ||||| || || ||||| || || |||||||| || || || |||||||| |||||||| |||||| | || |
---------------------gtctgtaatcaaacactgtatttatacactcacgtcagggaccatatgctctgtggaacttt---tttaccatttgggctcttgttgtacagGTTGATCGGGTCTTGTACTCGTCAGTGGTTTACCCCCACAACTACGGCTTCATCCCTCGAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGC
upper sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacaaaaccaattgcctggttattggaattgaagtctctacttactgccaaatgatttgtttcctatacacatctatctttatgcttacgattttcgaataattcatagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCTCATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
| | || | |||| | | || | |||| ||| | | || | ||| |||| | | || || | |||| |||||||||| || | || ||||||||||| || ||||| |||||||||||| | ||||||||| |||||||||||||||| || |||||||| || ||
------------------gttagatgagaacaaagtttattttttatat-gaatggttt-tcttatagcaaaatcaatctcaacaagtttgaattctc--tcattc--agGTTGATCGTATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCA
upper sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacaaaaccaattgcctggttattggaattgaagtctctacttactgccaaatgatttgtttcctatacacatctatctttatgcttacgattttcgaataattcatagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCTCATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
|| | || | || ||| | | | |||||| || || ||| | || | | ||| || | |||||||| || || | ||||| || ||||| |||||||| ||||| || ||| |||| |||||||| |||||||||||||| || || |||||||| |||
-------------------gtaaaaagatatcaaatcttgaaaaa--acagaatgatctga---------ggatatatgatgatcgtaagtgtttgtatatgtctatcagGTTGATAGGATTCTTTATTCTTCGGTTGTGTATCCTCACAACTACGGGTTTGTCCCACGCACACTATGTGAAGACAATGACCCTATAGATGTTTTAGTTA
upper sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------------------------gtacaaaaccaattgcctggttattgg-aattgaagtctctacttactgccaaatgatttgtttcctatacacatctatctt-----tatgcttacgattttcgaata---attcatagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCTCATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
| | | | || | | || || ||| | || || ||| | || | || | ||| | | | || | ||| | || | || | |||| || || || || |||||||| || || ||||||||||||||||| || || || || || || |||||||||||||||||| | |||||||| | |
gtaagactgaaccctgaagtgctttaatttccagacatttttccacatgatttggatatttgagcaccaaatcaccattgatggagatctgttttttcttccattttgttatgtatgcatgccttcatatgatgggaatgttttttctattgtttaacatcaatgcccagGTCGACCGTGTCTTATATTCATCTGTGGTGTATCCTCATAACTATGGATTCATTCCCCGTACCCTATGTGAAGACAATGATCCACTGGATGTTTTAATCC
upper sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 2
gtacaaaaccaattgcctggttattggaattgaagtctctacttactgccaaatgatttgtttcctatacacatctatctttatgcttacgattttcgaataattcatagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCTCATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
|| ||| |||| | | | ||| |||| ||| | ||| | ||| |||||||||| || | ||||| || || |||||||| || |||||||| ||| | || ||||| ||||||||||||||||| || |||| ||| | ||
---------------------------------------------gtgt-gaatagtttgatcttttctttcg-cta-ctttccagttatgctttggtcgttcttc-cagGTTGATCGAGTCCTTTATTCCTCGGTGGTTTATCCACACAACTATGGATTTGTTCCACGCACGCTGTGTGAAGACAATGACCCGCTTGACGTTCTTGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgtttcctatacacatctatctttatgcttacgattttcgaataattcatagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCTCATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
tgcttac putative branch site (score: 2)
attttcgaataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaaaaccaattgcctggttattggaattgaagtctctacttactgccaaatgatttgtttcctatacacatctatctttatgcttacgattttcgaataattcatagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCTCATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA