Sequence
atgc intronic sequence ATGC exonic sequencegttggtttggctcatttttatttttatcttgctttgattgatacatgataatgaatgatgctgttccatttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC
Basic information
species | Glycine max |
transcript | GLYMA15G04470.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 1
gttggtttggctcatt-----tttatttttatcttgctt--tgattgata--catgataatgaatgatgctgttccatttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC
|| | || |||||| || || ||| | | || |||| ||| | | | | || || || || ||| |||| || || ||||| || || ||||| || ||||||||||| || |||||||| || ||||||||||||||||| |||||||| ||||| || || |||||
gtcagctttcctcattgtaacttcatgtttctgtaactccatgatccataattttaacacagcataatattggtcaattgccagTTTATCCGGATGGACGTGTATGCATTTCTATTCTTCATCCGCCTGGTGATGATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATAC
upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
-----------gttggtttggctcatttttatttttatcttgctttgat-tgatacatgata--atgaatgatgct-gttccatttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC
|| || | | ||||||| || | | | || | ||| | ||| || || | | | |||| || || |||||||| ||||| || || |||||||||||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| ||||| || ||
gtcagctttttattagtgaaaattgtatttatttacttcatctgcagttctgttttctgacatcatgcataatatttgaggaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC
upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G007300_T02 (Zea mays), 3'ss of exon 3
-----------gttggtttggctcatttttattt---ttatcttgctttgattgatacatgataatgaatgatgct-gttccatttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC
|| || | | ||||||| ||||| || | | || ||| || | | | | | |||| || | ||||||| || || || || |||||||||||||| ||||| || |||| |||||||||||| ||||||||||| ||||| ||||| |||||
gtaagatttttattagtgaaagttgtatttatttagtttatccgctgttatgttttctgacatcatgcatattatttggggaaatgccagTTTATTCAGATGGGCTGGTGTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAGTGGTTATGAGCTCGCAAGTGAGCGTTGGACACCTGTGCATAC
upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
------------gttggtttg-gctcatttttatttttatcttgctttgattgatacatgataatgaatgatgctgttccatttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC
| || || ||||| | || | |||| || | ||| ||| | | | || ||| |||| || || |||||||| |||||||| || |||||||||||||| ||||| || || | |||||||||||||||||| || || ||||| || || || ||
gtaagcttcactatcggactgtactcatgtctact---atctgatcatgtcaaagttctgacaattcttattatt-ttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC
upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G012052_T01 (Zea mays), 3'ss of exon 3
gttggtttggc--tcat-ttttattt-ttatcttgctttgattgatacatgataatgaatgatgctgttccatttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC
|| | | || |||| | || | | ||| | || | ||| ||| | || | || ||| |||| || || ||||| || |||||||| || |||||||||||||| ||||| || || |||||||||||||||||||| || || ||||| || || || ||
gtaagcatcgctatcatgtcttgtctactatttgatcatgccaaagttctgacaattctttttgtt-ttgaattctcagTTTATCCTGATGGACGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAATGGTTATGAGCTTGCAAGCGAACGATGGACACCAGTGCACAC
upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g00910.t01 (Vitis vinifera), 3'ss of exon 3
gttggtttggctcatttttatt----tttatcttgctttgattgatacatgataa-tgaatgatgctgtt--ccatttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC
||| ||| | | |||||| ||| || | | || || || || | | | || | | | | |||| ||||| |||||| ||||||||| ||||| ||||| || || ||||||||||||||||| || ||||| |||| || |||||| | || || |||||
gttagttatagtgttctttattagagcatattttatgcttttgtgtaagggaaaagtgcttaaagttgctgtcaaactacagTTTACCCTGATGGGAAAGTTTGCATTTCAATCCTTCACCCCCCTGGTGATGACCCAAATGGCTACGAGCTGGCAACAGAACGCTGGTCCCCAGTCCATAC
upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 3
-------gttggtttggct-cat---ttttatttttatcttgctttgattgatacatgat----aatgaatgatgctgttccat---ttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC
||| || || ||| ||| |||||| || | |||| |||| ||| || | | || ||| || |||| || || ||||| ||||| |||||||||||||| ||||| || ||||| ||||||||||| ||||||||||||||||||||||||| ||| | |||||
gttggttgtttgtccaactgcatgtgtttgatttttgactc-ttaccattggagcatggcttgaaatcaacttggttcttgcatgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC
upper sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------gttggtttggctcatttttatttttatcttgctttgattgatacatgataatgaatgatgctgttccatttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC
| | || || | |||| | |||| || | || || | | ||| | || || ||| |||||| || || ||||| || |||||||| |||||||| ||| | || |||||||| |||||||||||||| | || |||||||| ||| | || || |||||
gaaagaactctggtttgactctgaatgcactcatgtgacttaatttt-tctttacgatgttctgcttatttcc--ataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATACMapped 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|254336753|gb|GR842932.1|GR842932EST: AAATAGTCCGCCATCAGTGAAATTTACCTCAGAGTTATGGCATCCCAATG TGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATG
genomic: AAATAGTCCGCCATCAGTGAAATTTACCTCAGAGTTATGGCATCCCAATGgttggtttgg ... ccatttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttatcttgctttgattgatacatgataatgaatgatgctgttccatttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC
gattgat putative branch site (score: 4)
ttccattt putative PPT
ataatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtttggctcatttttatttttatcttgctttgattgatacatgataatgaatgatgctgttccatttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA