Sequence
atgc intronic sequence ATGC exonic sequencegtttttaatagtcctaaactctaccatggtgcattctcttggctctagtgttttctttgttgacatttaatttatatacgcagCAAGTATACATGTACTTCCGGGGCAGTGGAAAGGCTGCAGCGATGAGGCGTGAAGCTGCGCAAGGGGCCATGAGGGCAGCTCTA
Basic information
species | Glycine max |
transcript | GLYMA12G32860.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 11
--------------------gttttta-atagtcctaaactctaccatggtgcattctcttggctctagtgttttctttgttgacatttaatttatatacgcagCAAGTATACATGTACTTCCGGGGCAGTGGAAAGGCTGCAGCGATGAGGCGTGAAGCTGCGCAAGGGGCCATGAGGGCAGCTCTA----------------
|| ||| ||| | || | | | || | | | | ||| | | |||| | | | | | | |||||||||||||||||||||||| || |||||||| || |||| ||||| ||||| || || | || || |||| | || |
aggttcaacatagcatggacattcttacatacatttcaatcgtttcttagtcaaattttc--attttag-atcatgaccattgattgctcactca-acatgcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCCGCAGAGATGAAACGTGAGGCGGCACGTGGTGCTCTGAGCTCCGCATTCTGATGAAACATGCCTT
upper sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 12
-------------------------------------------------------------------------------------------------gttttta-atagtcctaaactctaccatgg------tgcattctcttgg--------ctctagtgttttctttg--ttgacatttaatttatatacgcagCAAGTATACATGTACTTCCGGGGCAGTGGAAAGGCTGCAGCGATGAGGCGTGAAGCTGCGCAAGGGGCCATGAGGGCAGCTCTA----------------
|| | || | |||| || | | || | || | || | || ||| ||| | | | || | | |||| | | ||||||||| |||||||||||||| || |||||||| ||||| | ||||| |||||| || | || || ||| |||||||| |
gtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgtttttatgaaataaattctcaagtagtctatctgagccgttttgacatttgtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGTGATGCAACTAGGGGTGCTATGCGGGCAGCTTTTTAATTATCAGAAAAGA
upper sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
------------gtttttaatagtcctaaact----ctaccatggtgcattctcttggctctagt-gttttctttgttgacatttaatttatatacgcagCAAGTATACATGTACTTCCGGGGCAGTGGAAAGGCTGCAGCGATGAGGCGTGAAGCTGCGCAAGGGGCCATGAGGGCAGCTCTA----------------
||| || | ||| | || | ||| || ||| || || | | | || || | || | || | | |||||||||||||||||| ||||| || ||||| |||||||| | ||||| ||||| || || | || || ||||| | || |
ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgtcattctgaacttggccgtttgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG
upper sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
gtttttaatagtcctaaactctaccatggtgcattctct----tggctctagtgttttctttgttgacatttaatttat-atacgcagCAAGTATACATGTACTTCCGGGGCAGTGGAAAGGCTGCAGCGATGAGGCGTGAAGCTGCGCAAGGGGCCATGAGGGCAGCTCTA----------------
| | | | ||| || ||| | | || || || ||||| | | | || | | ||||||||| |||||||||||||| || |||||||||||||||| ||||| |||||| || || || || ||||| || || |
---gtcagtt-ttctattatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagccctttttggaccgcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA
upper sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
----------------------------------------------------------------------------gtttttaata-gtcctaaactctacc-atggtgcattctcttggctctagtgttttctttgttgacatttaatttatatacg---cagCAAGTATACATGTACTTCCGGGGCAGTGGAAAGGCTGCAGCGATGAGGCGTGAAGCTGCGCAAGGGGCCATGAGGGCAGCTCTA----------------
| | | || || ||| |||| | | | || | | || | | | || | || | | | | ||||||||||||||||||||||| || |||||||| ||||||| ||||| ||| || || || | || || |||||| || |
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattattgttctgaacttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG
upper sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 11
------------------------------------------------------------------------------------gtttttaatagtcctaaactctacca--tggtgcattctcttggctctagtgttttctttgttgacatttaatttatatacgcagCAAGTATACATGTACTTCCGGGGCAGTGGAAAGGCTGCAGCGATGAGGCGTGAAGCTGCGCAAGGGGCCATGAGGGCAGCTCTA----------------
| | | || || | | ||| ||| | || |||| | | ||| | || | | | | | | |||||||||||||||||| ||||| || |||||||| ||||||| ||| | ||||| || || | | || | || |||| |
gttggttgaatctgttctttgttcaataaatcctccatcatacagtttgagaaaaaaaaagcaatccgtcatcatagaacccagggatctcattgtgcattattcttccatttattgagttctttatgttcttcacacctgaccattaagttctctctca-acttgcagCAAGTATACATGTATTTCCGTGGAAGTGGAAAAGCTGCAGAGATTAAACGTGAGGCAGCACGTAGTGCTCTAAGTTCAGCCTTCTGATGAACATCTTTTT
upper sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 11
-------------gtttttaatagtcctaaactctaccatggtgcattctcttggctctagtgttttct----ttgttgacatttaatttatatacgcagCAAGTATACATGTACTTCCGGGGCAGTGGAAAGGCTGCAGCGATGAGGCGTGAAGCTGCGCAAGGGGCCATGAGGGCAGCTCTA----------------
||| || | | || | | | | || | || | |||| | || | ||| ||| ||||||||| |||||||||||||| |||||||| |||||| || ||| | |||||| || || |||| | | | | ||| |
gttcagtagtctgatttctagttcttctgcttctatctccagcacttctactgcatcttggtttcttctaactctctttgttctcaatcccaatatgcagCAAGTTTACATGTACTTCCGAGGCAGTGGCAAGGCTCAAGAGATAAAGCGTGATGCGGCAAGAGGGACTGTAATGCAAGCATTTTGATGTGCCACGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgcattctcttggctctagtgttttctttgttgacatttaatttatatacgcagCAAGTATACATGTACTTCCGGGGCAGTGGAAAGGCTGCAGCGATGAGGCGTGAAGCTGCGCAAGGGGCCATGAGGGCAGCTCTA
ttttctttgttgacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttaatagtcctaaactctaccatggtgcattctcttggctctagtgttttctttgttgacatttaatttatatacgcagCAAGTATACATGTACTTCCGGGGCAGTGGAAAGGCTGCAGCGATGAGGCGTGAAGCTGCGCAAGGGGCCATGAGGGCAGCTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC