Sequence
atgc intronic sequence ATGC exonic sequence...ttcatataaaattcaggttgtaccttttggctgtataatatttttgtttatctttatgtattatcaaataatgtttgaaaaactctaaattttactgtagCTTTACAAGATCTTGAAGGAGCATAAGAATCCTAAGGTTCTTAGTGAGGGAATTTTGTGGATGGTTTCTGCTGTTGAAGATTTTGGTGTCTCACATATAA
Basic information
species | Glycine max |
transcript | GLYMA20G32430.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 21
-------------------------------------ttcatataaaattcaggttgtaccttttggctgtataatatttttgtttatctttat---gtattatcaaataatgtttgaaaa--actctaaattttactgtagCTTTACAAGATCTTGAAGGAGCATAAGAATCCTAAGGTTCTTAGTGAGGGAATTTTGTGGATGGTTTCTGCTGTTGAAGATTTTGGTGTCTCACATATAA
| | || || | || || | |||||| ||| || ||| || || | | || ||| ||| || | | | | | ||||| ||||| || |||| ||||| || ||||| ||||| ||||| ||||| ||| | |||||||||||||| ||||| || ||||| |||| || |||
gtaagagaaaacactatcggaagtccaaacagttcaatatccgtgaagatcctttagttatttacaa-taaataatagtttacttgcccttaatcaggtgatgttaagtaactgttgtaatttatgcctttctcttttatagCTATACAAAATAATGAAAGAGCACAAAAATCCAAAGGTGCTTAGCGAGGGTATTCTTTGGATGGTTTCTGCCGTTGAGGACTTTGGGATCTCCAATTTAA
upper sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 21
----ttcatataaaattcaggttgtaccttttggctgtataatatttttgtttatctttatgtattatcaaataatgtttgaaaaactctaaattttactgtagCTTTACAAGATCTTGAAGGAGCATAAGAATCCTAAGGTTCTTAGTGAGGGAATTTTGTGGATGGTTTCTGCTGTTGAAGATTTTGGTGTCTCACATATAA
|| | | |||| || || | | | | | | | | |||| || ||| || | | | | | | | | ||||| ||||||||||| || |||||||||| |||||||| ||||||||||||||||| ||| | |||||||| |||||||| ||||| ||||| |||| || |||
cactgtcgaacatctttcaattttattctgtgctttaggtgcacgctgcttccaccatgatgt-ttgacaactactatatttatgagttttattttta---tagCTTTACAAAATAATGAAGGAGCACAAGAATCCCAAGGTTCTTAGTGAGGGTATTCTTTGGATGGTCTCTGCTGTGGAAGACTTTGGGATCTCCAATTTAA
upper sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------------------ttcatataaaattcaggttgtaccttttggc---tgtataatatttttgtttat-ctttatgtattatcaaataatgtt-tgaaaaactctaaatttta---ctgtagCTTTACAAGATCTTGAAGGAGCATAAGAATCCTAAGGTTCTTAGTGAGGGAATTTTGTGGATGGTTTCTGCTGTTGAAGATTTTGGTGTCTCACATATAA
| | | |||||||| ||| | | | | | | | ||||| ||| | ||||| | | | || | || | || | | | ||||| ||||||||||||| || |||||||||| |||||||| |||||||||||||| || ||| | |||||||| |||||||| ||||| ||||| |||| || |||
gtaagagataccattagattattattgtttttgttcaaaaggtcctccacatttgttcaatcaacccaattaggtgattttatatgctggtccgcaataaattcagaatgtgcactgtcgaacatctttgcaattttattttgtgctttagatgcacactgcttatatgatgtataattatgagttttaattttgtagCTTTACAAAATAATGAAGGAGCACAAGAATCCCAAGGTTCTTAGTGATGGTATTCTTTGGATGGTCTCTGCTGTGGAAGACTTTGGGATCTCCAATTTAA
upper sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 12
-----------------------------------------------------------------------ttcatataaa-attcaggttgtaccttt-tggctgtata-atattt-ttgtttatctttat----gtattatcaa----ataatgtttgaaaaactctaa-attttactgtagCTTTACAAGATCTTGAAGGAGCATAAGAATCCTAAGGTTCTTAGTGAGGGAATTTTGTGGATGGTTTCTGCTGTTGAAGATTTTGGTGTCTCACATATAA
|| |||| || || |||| || | | | ||| |||| | ||| || || | ||| | | | | || ||| | | | ||| | ||||||||||| ||| |||| ||||| |||||||| ||||| ||||||||||| || |||||||||||||| || |||||||| |||||||| |||||| | |
gtaagtcaagtttctatcgggcttgaagcttctgtttctctatttggtttgatataaaaacttccttagaattaatatttttatatagattgtgtctatactgaagcatagatatctattggccattgttgtttcagtaatcttgacttggtcatatttttctatggatgatgcttttttatagCTTTACAAAATCATGAAAGAGCACAAGAATCCAAAGGTCCTTAGTGAGGGCATCTTGTGGATGGTTTCAGCAGTTGAAGACTTTGGTGTTTCACATTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttatctttatgtattatcaaataatgtttgaaaaactctaaattttactgtagCTTTACAAGATCTTGAAGGAGCATAAGAATCCTAAGGTTCTTAGTGAGGGAATTTTGTGGATGGTTTCTGCTGTTGAAGATTTTGGTGTCTCACATATAA
ctctaaa putative branch site (score: 3)
ttttact CT-rich tract
tattatcaaataatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcatataaaattcaggttgtaccttttggctgtataatatttttgtttatctttatgtattatcaaataatgtttgaaaaactctaaattttactgtagCTTTACAAGATCTTGAAGGAGCATAAGAATCCTAAGGTTCTTAGTGAGGGAATTTTGTGGATGGTTTCTGCTGTTGAAGATTTTGGTGTCTCACATATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - -gtacctt
- - - - - - - - - - - - - -tggctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgtttg