Sequence
atgc intronic sequence ATGC exonic sequencegtattgatttcttctcttaaaaactaaaaagaaaaaaattgatgctatcaattttgttcggtttgacaagatgtaagatttgaagtgtggcactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAACAATGGCTGCATGGGGATGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC
Basic information
species | Glycine max |
transcript | GLYMA18G47170.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47170.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g03410.1 (Oryza sativa), 3'ss of exon 2
gtattgatttcttctcttaaaaactaaaaagaaaaaaattgatgctatcaattttgttcggtttgacaagatgtaagatttgaagtgtggcactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAACAATGGCTGCATGGGGATGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC
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-----------gtacaatgaaatctcttcatcaattttgtg-cattattattccctctctgattaatg-gatgttttactcacattgccgttttggttgaacagGATGCTCGTGTATGAATATGTAGACAACGGCAATCTTGATCAATGGCTTCATGGTGATGTAGGGGAAGTGAGCCCACTAACTTGGGAAGTCAGGATGAAC
upper sequence: GLYMA18G47170.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 2
----------gtattgatttcttctcttaaaaactaaaaagaaaaaaattgatgctatcaattttgttcggtttgacaagatgtaagatttga---agtgt-ggcactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAACAATGGCTGCATGGGGATGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC
||||| | ||| |||| | | | | | || ||| ||| | | | || | |||| | ||| | | || || |||||||||||||||| |||||||| |||||||| ||||| || || ||||| ||||| |||||||||| |||||||| | |||||| || | ||||||||
gtatgatggcatattgctatctcttcttca---ttcggtccggtgacacc--tactctcagtttggattctcaataatggaagcctgattcctgtcactgtcgtctatgcttgaacagGATGCTTGTGTACGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGAGAAGTAAGCCCACTAACATGGGACGTCAGGATGAAC
upper sequence: GLYMA18G47170.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G317938_T01 (Zea mays), 3'ss of exon 2
------------------gtattgatttcttctcttaaaaactaaaaagaaaaaaattgatgctatcaattttg--ttcggtttgacaagatgtaagatttgaag--------tgtgg-cactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAACAATGGCTGCATGGGGATGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC
|||| ||| |||| | | ||| | || ||||||| | ||| ||| | | | || | | ||| | || || |||||||||| |||||||||||||| |||||||| ||||| || || ||||| ||||| |||||||| | || ||||| |||||||| |||| ||||||||
gtatgtgtgttggcaggcacattgcaatctcttcttcgt--tcggtggacacctagttgcttctctcaatttagggttctcaatgatggaagcttgcttctgtatatcactactatggtctatgcttgaacagGATGCTCGTGTATGAGTATGTGGACAATGGTAATCTTGACCAGTGGCTTCATGGTGATGTTGGCGAAGTGAGCCCACTGACATGGGACATCAGGATGAAC
upper sequence: GLYMA18G47170.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g02030.t01 (Vitis vinifera), 3'ss of exon 2
gtattgatttcttctcttaaaaactaaaaagaaaaaaattgatgctatcaattttgttcggtttgacaagatgtaagatttgaagtgtggcactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAACAATGGCTGCATGGGGATGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC
|||||| | | | ||||| | | | | | | | | ||| | | | ||| | ||| | || || ||||||||||||||||||||||| |||||||| ||| | || || ||||| ||||||||||| || | || |||||| |||||||| | || ||||| |||
gtattgctacccatcttc---tgctaaatcctgacactgggttttcttgaggatccaaaaaactaacattttttcatctttcatttgttttttttttgtc-tagGATGCTTGTGTATGAGTATGTGGACAATGGTAATTTGGACCAGTGGCTTCATGGGGATGTAGGGGAAGTCAGCCCTCTGACATGGGATATTCGGATTAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattttgttcggtttgacaagatgtaagatttgaagtgtggcactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAACAATGGCTGCATGGGGATGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC
gtttgac putative branch site (score: 4)
ctgttttc putative PPT
taagattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgatttcttctcttaaaaactaaaaagaaaaaaattgatgctatcaattttgttcggtttgacaagatgtaagatttgaagtgtggcactgttttcacagGATGCTTGTGTATGAGTATGTAGACAATGGCAATCTAGAACAATGGCTGCATGGGGATGTTGGAGCTGTAAGCCCTTTGACATGGAACATACGGATGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA