Sequence
atgc intronic sequence ATGC exonic sequence...gttgaattttgtttgtggtgtttcttttttcatgacttgttttgttctatgtatggtttgttggttgcatgtcttattttgatgtttggtcataaatgcaGTGTCTGGGTTGCTCGTAGACCACCAGGATATGCATTTATTGAGTTTGATGATCGGAGGGATGCACTTGATGCAATTCAGGCCTTGGAT
Basic information
species | Glycine max |
transcript | GLYMA18G18860.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G18860.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g54770.1 (Oryza sativa), 3'ss of exon 2
----gttgaattttgtttgtggtgtttcttttttcatgacttgttttgttctatgtatggtttgttggttgcatgtcttattttgatgtttggtcataaatgcaGTGTCTGGGTTGCTCGTAGACCACCAGGATATGCATTTATTGAGTTTGATGATCGGAGGGATGCACTTGATGCAATTCAGGCCTTGGAT-
||| | | ||||| ||| | || | || ||| | | || ||| |||| |||| | | ||||| | || | | | |||||||||||||||||| |||| |||||| || | ||||||||| || |||||||| ||||||||| |||||| | | | || |||
tattcctgactcaatatagtggtaccccttgtactataagttatttggacgt-tgcg-ggtatgtttgttg---atgtaattttcaagtgtatttttccatgcagTGTCTGGGTTGCCCGTAAACCACCTGGTTTTGCATTTATCGATTTTGATGACAAGAGGGATGCTGAGGATGCACTCCGTGATTTAGATG
upper sequence: GLYMA18G18860.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G151923_T01 (Zea mays), 3'ss of exon 2
-gttgaatttt---gtttgtggtgtttcttttttcat-gacttgttttgttctatgtatggtttgttggttgcatgtcttattttgatgtttggtcataaatgcaGTGTCTGGGTTGCTCGTAGACCACCAGGATATGCATTTATTGAGTTTGATGATCGGAGGGATGCACTTGATGCAATTCAGGCCTTGGAT-
| ||| | | | | || | | || ||| || | | || | ||| || | || | | || ||| |||| |||||| | | | ||||||||||||||||||| | |||||| || | ||| |||||||| ||||||||| |||||| ||| |||||||| | | | | |||
tatataatcgttgaatgcatagaattacatcttgcattgatatatgctgcttgatgc-tgatgattttggtaca---ctttttttcatgttt--ttgtggaagcagTGTCTGGGTTGCTCGGAAACCACCTGGCTTTGCGTTTATTGATTTTGATGATAAGAGGGACGCAGAGGATGCAATCCGTGACCTAGATG
upper sequence: GLYMA18G18860.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G080930_T01 (Zea mays), 3'ss of exon 2
gttgaattttgtttgtggtgtttcttttttcatgacttgttttgttctatgtatggtttgttggtt-gcatgtcttattttgatgtttg--gtcataaatgcaGTGTCTGGGTTGCTCGTAGACCACCAGGATATGCATTTATTGAGTTTGATGATCGGAGGGATGCACTTGATGCAATTCAGGCCTTGGAT-
| |||| |||| | || || | | || ||||| ||| | |||||||| || | || | | | | || || | |||||||||| ||| |||| |||| |||||| || | |||||||||||| ||||| || |||||||||| ||||| |||| | | |||
--taggttttacttgttgcgtcctttgcgttttttttttctttgtgagatgga--gtttgttgtttcacctggtgcaggtcgctaactgttgttctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG
upper sequence: GLYMA18G18860.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0026g00250.t01 (Vitis vinifera), 3'ss of exon 1
--gttgaattttgtttgtggtgtttcttttttcatgacttgttt-tgttctatgtatggtttgttggttgcatgtcttattttgatgtttggtcataaatg-caGTGTCTGGGTTGCTCGTAGACCACCAGGATATGCATTTATTGAGTTTGATGATCGGAGGGATGCACTTGATGCAATTCAGGCCTTGGAT-
|| || ||| | | | | | || |||| || | | || | || | || |||| |||||| ||||| | | | | | |||||| ||||||||||| |||||||| || ||||| ||| ||||||||| |||||| |||||||| | |||||||||| | ||||||
tttttaaaacttgatactattttcaacacatagattactttttagtatcctgcatttgaaatttttgttg---gtcttaacac-atgtt-gctaaaatttatcagTGTTTGGGTTGCTCGGAGACCACCGGGTTATGCTTTTGTTGAGTTTGCTGATCGTAGGGATGCTGTAGATGCAATTCGTGGATTGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctatgtatggtttgttggttgcatgtcttattttgatgtttggtcataaatgcaGTGTCTGGGTTGCTCGTAGACCACCAGGATATGCATTTATTGAGTTTGATGATCGGAGGGATGCACTTGATGCAATTCAGGCCTTGGAT
ttttgat putative branch site (score: 4)
ttattttgatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgaattttgtttgtggtgtttcttttttcatgacttgttttgttctatgtatggtttgttggttgcatgtcttattttgatgtttggtcataaatgcaGTGTCTGGGTTGCTCGTAGACCACCAGGATATGCATTTATTGAGTTTGATGATCGGAGGGATGCACTTGATGCAATTCAGGCCTTGGAT
- - - - - - -tgtggtg
- - - - - - - - - - - - - - -tcatgac
- - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - -tgtatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtttg