Sequence
atgc intronic sequence ATGC exonic sequence...tgaagactgtaaaccaactatcagcttgctggtattatctaataatttaggtgctgttaccatgaaagaatattgagggaacatttcaattgttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAGTTGCGGCTGGAATGAATGCAATGGACCTGAGGCGTGGTATAAG
Basic information
species | Glycine max |
transcript | GLYMA10G25630.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 4
tgaagactgtaaaccaactatcagcttgctggtattatctaataatttaggtgctgttaccatgaaagaatattgag-ggaacatttcaatt-gttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAGTTGCGGCTGGAATGAATGCAATGGACCTGAGGCGTGGTATAAG
| | || ||| | |||| | || | | |||| | | | || | | | | ||| || | |||| ||||| || ||||| || | || ||||||||||||||| || ||||| || ||||| ||||| |||||||||||||| | |||||||||||
tatttgcacaaattcaatatgtggattgc--attgtactttaggatttgcttagttgcataatttgtttgttctaactgtgttattctgatccaaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCAAGTCTGTTGCTGCTGGCATGAATGCAATGGATTTAAGGCGTGGTATTTC
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 3
-----tgaagactgtaaaccaactatcagcttgctggtattatctaataatttaggtgctgttaccatgaaagaatat-tgagggaacatttcaattgttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAGTTGCGGCTGGAATGAATGCAATGGACCTGAGGCGTGGTATAAG
| | ||||| | ||| ||| || ||| | | || || | || || | | | || || ||| | || || || |||| ||||| || ||||| || | ||| ||||||||||||||| || |||||||| |||||||||||||||||||||||||| | |||||||| ||
tgaccggtctaacataaactatgcctcatattgttga-attgtatg-tagctt-gttgatgctttcttcgaactgtacgtgatctgatatccaaaaaatt---cagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGTGGAATCTC
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 3
--tgaagactgta--aaccaactatcagcttgctggtattatctaataatttaggtgctgttaccatgaaagaatat-tgagggaacatttcaattgttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAGTTGCGGCTGGAATGAATGCAATGGACCTGAGGCGTGGTATAAG
|||| |||| || | | | | | ||| | | || || | || ||| | | || || ||| |||| ||| ||| |||| ||||| || || || || | ||| ||||||||||||||| || |||||||| |||||||||||||||||||||||||| | ||||| || ||
attgaatcatgtaataagttaaattttctatatttgaattgtatg-tagctt-gctgatgtcttcttccaactgtacctgatctgacatc-caaaaattt--cagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGCGGAATCTC
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------tgaagactgtaaaccaactatcagctt--gctggtattatc--taataatttaggtgctgttacca-----tgaaagaatat-tgagggaacatttcaattgttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAGTTGCGGCTGGAATGAATGCAATGGACCTGAGGCGTGGTATAAG
| | | |||| | || | || ||| | | || | || | || || | || ||| ||| || || | || || ||||||| ||||| || ||||||||||| |||| || || || ||||| || ||||||||||| ||||||||||||||||||||||| || |||||||| |
gtaagtgttccctttcaatggattaaaacgttttttctgtttttgctaattgggttgttagtctcctatctactcatattaatcggtgtttttgtatctgacaaaatatatggtatgcgttacagGAACAACGTGTGCCACAGTCCTTACTAGAGCTATCTTCACGGAAGGTTGTAAATCAGTTGCCGCTGGAATGAATGCAATGGACCTAAGACGTGGTATCAA
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 3
tgaagactgtaaaccaactatcagcttgctggtattatctaataatttaggtgctgttaccatgaaagaatat---tgagggaacatttcaattgttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAGTTGCGGCTGGAATGAATGCAATGGACCTGAGGCGTGGTATAAG
|||| | | ||| ||| | | ||||| | ||| || | || || || | ||| | | ||| | |||| |||||| || || || ||||| ||||| || || || |||||| | ||||| |||||||||||||| || |||||||||||||||||| || | | |||||
--------gtaagata--tttcattttgattg-attatgcggtt-catagttgtagaaactttgcaaaactatgtaccaatgcttgtttaacttgtcatgcagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCAAATCAGTTGCCGCAGGAATGAATGCAATGGACTTGCGAAGAGGTATTTC
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------------------------tgaagactgtaaaccaactatcagcttgctggtattatc--taataatttaggtgctgttaccatgaaagaat-attgagggaacatt---tcaattgttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAGTTGCGGCTGGAATGAATGCAATGGACCTGAGGCGTGGTATAAG
| | ||| | | | | | || | | | | | | |||| | | | | || ||| | |||||| | || |||||||||||| || ||||| || |||||||| || ||| ||||||| ||||||||||| || ||||| ||||| ||||||||| || | | || || |
gcaagtgctctgtgtcatataatttgtgaagtttgagttcttagtcaggagcattattttcttgaatattgcagggtctaccgtattcaatctaatgacgacacatttag-acgtgattatagacactgttcgtggttgtttaactatccgattcgtactgggatcatttggctaacattggctgaaacaccctgcagGAACCACTGCTGCAACAGTGCTCACACGAGCTATTTTTGCTGAAGGGTGCAAATCAGTAGCAGCTGGTATGAACGCAATGGACTTGCGCAGGGGCATCAA
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------------------tgaagactgtaa-accaactatcagct-tgctggtattatctaataatttaggtgctgttaccatgaaagaatattgagggaac-atttcaattgttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAGTTGCGGCTGGAATGAATGCAATGGACCTGAGGCGTGGTATAAG
||| ||| | | || | || || | |||| || | ||| | | | || ||| || || || | | | | | | |||||||||||| || || || ||||| || || |||||||| ||| ||| ||||||||||||||||| ||||| ||||| ||||||||||| | | ||||| ||
gtatatgcctaatcccagttgactgtgtgaacctcgttctgatgcatgatttcaacctactttttcattttgtatgaatctatggaatactcttatacagattaacatcagcactggccttgccaaatcaat-aaatgtatctacagtgcaatgatttcactgactcgaagttatgaattttgcagGAACAACTTGTGCAACAGTGCTCACCCGAGCAATTTTTGTTGAGGGCTGCAAATCAGTTGCAGCTGGCATGAACGCAATGGACCTACGTAGAGGTATTAG
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 3
-tgaagactgtaaaccaactatcagcttgctggtattatc-taataatttaggtgctgttaccatgaaagaatattgagggaacatt--tcaattgttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAGTTGCGGCTGGAATGAATGCAATGGACCTGAGGCGTGGTATAAG
|| | | ||||| | | |||| | | ||||||| || ||| || ||| || | ||| | || | ||||||||| || || ||| ||||| ||| | ||||| || ||||||||||| ||||| || ||||| ||||| |||||||| |||||| || | ||||| || |
ctgggtgacatgagccaacagttggaaga--agtatcagggtttcaatttagaggcga--accgcaaatgaacgttaaactgacagtaacgaacttttttgcagGTACAACTGCCGCAACAGTGCTTGCTCGAGCCATTTTTACTGAAGGTTGCAAGTCCGTTGCAGCTGGCATGAATGCCATGGACTTGCGCCGTGGCATTACMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|192326682|gb|FK018869.1|FK018869EST: CAGTCTTGTAAAGCAGGTTGCAAATGCTACTAACGATGTGGCTGGTGATG GAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCA
genomic: CAGTCTTGTAAAGCAGGTTGCAAATGCTACTAATGATGTGGCTGGTGATGgtaagctgat ... tgttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCA
EST:
gi|16276997|gb|BI942150.1|BI942150EST: CAGTCTTGTAAAGCAGGTTGCAAATGCTACTAATGATGTGGCTGGTGATG GAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCA
genomic: CAGTCTTGTAAAGCAGGTTGCAAATGCTACTAATGATGTGGCTGGTGATGgtaagctgat ... tgttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaggtgctgttaccatgaaagaatattgagggaacatttcaattgttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAGTTGCGGCTGGAATGAATGCAATGGACCTGAGGCGTGGTATAAG
ttgtttt CT-rich tract
atttcaattgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaagactgtaaaccaactatcagcttgctggtattatctaataatttaggtgctgttaccatgaaagaatattgagggaacatttcaattgttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAGTTGCGGCTGGAATGAATGCAATGGACCTGAGGCGTGGTATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - gactgta
- - - - - - -ccaacta
- - - - - - - - - - - -gcttgct
- - - - - - - - - - - - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagggaa