Sequence
atgc intronic sequence ATGC exonic sequence...ttgttgttttgtcctgttttgagatctttatcaatatttctgtattatgcaccttcctttttcaatagtctttttttatctgtttgatggcttttggcagGTCCTTATCATGGTGGTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGATTTATCAACAAGATCTATCACCC
Basic information
species | Glycine max |
transcript | GLYMA09G39370.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39370.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 2
ttgttgttttgtcctgttt--tgagatctttatcaatatttctgtattatgcaccttcctttttcaatagtctttttttatc--tgtttgatggcttttggcagGTCCTTATCATGGTGGTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGATTTATCAACAAGATCTATCACCC
| ||| |||| || | || | | | || | ||| | | || | | | | || |||||| | ||| ||||||| |||||| |||||||| ||||| || ||||| || ||||| ||||| ||||||||||||||||| || ||||| || | |||||||| ||||| ||
---tgaattttgcctgcttgttcagttgaccaggagtagtcttgtttcagtgactggggaagagaagatatggagtctgatgaatgtttgcttaattt-ggcagGTATTTATCAAGGTGGTGTCTGGAAGGTTAGAGTAGAATTGCCTGATGCATATCCTTACAAATCTCCGTCGATTGGTTTCGTTAACAAGATTTATCATCC
upper sequence: GLYMA09G39370.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 2
ttgttgttttgtcctgttttgagatctttatcaatatttctgtattatgcaccttcctttttcaatagtctttttttatctgtttgatggct--tttggcagGTCCTTATCATGGTGGTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGATTTATCAACAAGATCTATCACCC
| | ||| ||| | || | || || | | | ||| ||| | ||| | || | ||||| |||| || || || ||||| ||||| || || || || |||| ||||| |||||||||||||| || ||||| || || ||||||||||| ||||||||
tcatc--cttgattggttgctcagttgacccgaaccgtccttccttttcagtcatagtttatcacaggattttgccaaataaattcgtactcaatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCC
upper sequence: GLYMA09G39370.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T01 (Zea mays), 3'ss of exon 2
---ttgttgttttgtcctgttttgagatctttatcaatatttctgtattatgcaccttcctttttcaatagtctttttttatctgtttg-atggcttttggcagGTCCTTATCATGGTGGTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGATTTATCAACAAGATCTATCACCC
| ||| || || || | | | | | | ||| | | | || | || | | | || || || | | | ||||| |||| || || || ||||| ||||| || || || || |||| ||||| |||||||||||||| || ||||| || || ||||||||||| ||||||||
tcatccttgattggt--tgctcagttgacccgaaccgtccttccttttcagtcatagt--ttatcacaggattttgccaaataaattcgcactccatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCATATCCTTACAAATCCCCGTCCATCGGCTTCATCAACAAGATTTATCACCC
upper sequence: GLYMA09G39370.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G150867_T03 (Zea mays), 3'ss of exon 1
ttgttgttttg-tcctgttttgagatctttatcaatatttctgtattatgcaccttcctttttcaatagtctttttttatc--tgtttgatggcttttggcagGTCCTTATCATGGTGGTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGATTTATCAACAAGATCTATCACCC
| | || | || | | | ||| | | | ||| | || | | | | | |||| | || | || ||| |||||| || ||| | |||| || ||||| || |||| ||||| |||||||||||||| || || ||||| || ||||| ||||| ||||||||
--actatcttaatgttgcacttaaagcttcagtcttgtc-ctgcactagtgatttaggagggctggctgcactatcttatggatactttgctgaattcaatagGCATTTATCAAGGAGGTATATGGAGGGTTAGAGTAGAACTGCCAGATGCGTATCCTTACAAATCCCCATCGATTGGTTTCATCAATAAGATATATCACCC
upper sequence: GLYMA09G39370.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S161_122V6.1 (Physcomitrella patens), 3'ss of exon 2
ttgttgttttgtcc-tgttttgagatctttatcaatatttctgtattatgcaccttcctttttcaatagtctttttt--tatctgtttgatggcttttg-gcagGTCCTTATCATGGTGGTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGATTTATCAACAAGATCTATCACCC
|| ||| | |||| | || || | | | | | | || || || || ||| | | || | | ||| ||||||| ||||| | || |||||| | ||||||| ||||| ||||||||||| |||||||||||||||||||| ||| | |||| ||||| || ||
----tgagttgcacacatttttgtgtattccgaaactgggattcgtcgttctctatatattggtaaaagcctgacgagacatcggatgaatcggtgttgcacagGTCCATATCAAGAAGGGACCTGGAAAATCCGAGTTGAATTGCCCGATGCTTATCCCTACAAATCTCCTTCCATTGGGTTTGTGAACAGGATCTTCCATCC
upper sequence: GLYMA09G39370.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 2
ttgttgttttgtcctg--ttttgagatctttatcaatatt-tctgtattatgcaccttcctttttcaatagtctttttttatctgtttgatggcttttggcagGTCCTTATCATGGTGGTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGATTTATCAACAAGATCTATCACCC
||| |||| | | ||| | || | | | || | | || | | | || | ||||| | | || | | | || | |||||||||||||| || | || ||||| | |||| || ||||| ||||||||||| ||||| |||||||||||||| ||| | || | ||||| || ||
---ttggtttgctcagactttcgtgacttacaggattaggatttacttttctcttcatatttgtgcaatactgatgccatagcggatgaattggggttggcagGTCCTTACCAAGAAGGAACCTGGAAGATCCGAGTCGAATTGCCTGATGCTTATCCCTACAAGTCTCCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCMapped 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|254327211|gb|GR836820.1|GR836820EST: TCCATGGACCCAATGACA GTCCTTATCATGGTGGTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTT
genomic: TCCATGGACCCAATGACAgtgagttccc ... cttttggcagGTCCTTATCATGGTGGTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgcaccttcctttttcaatagtctttttttatctgtttgatggcttttggcagGTCCTTATCATGGTGGTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGATTTATCAACAAGATCTATCACCC
gtttgat putative branch site (score: 5)
ctttt putative PPT
tttttcaatagtcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttgttttgtcctgttttgagatctttatcaatatttctgtattatgcaccttcctttttcaatagtctttttttatctgtttgatggcttttggcagGTCCTTATCATGGTGGTGTGTGGAAAGTAAGAGTTGAGTTGCCGGATGCTTATCCTTACAAATCTCCTTCCATTGGATTTATCAACAAGATCTATCACCC
-tgttgtt
- - - - -tgtcctg
- - - - - - - - - - - - - - - - - - -ttctgta
- - - - - - - - - - - - - - - - - - - - - - ttatgca
- - - - - - - - - - - - - - - - - - - - - - - - - -ccttcct