Sequence
atgc intronic sequence ATGC exonic sequence...atttccttgacttgtgcttttgtttctttgtttatactttttctgctcttatacagttatacttccgttggtaccttactggttttgatttaattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATTAGTGCCATGATACTTGGTGGAACAATGG
Basic information
species | Glycine max |
transcript | GLYMA08G24120.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 7
----atttccttgacttgtgcttttgtttctttgtttata-ctttttctgctcttatacagttatacttccgttggtaccttactggttttgatttaattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATTAGTGCCATGATACTTGGTGGAACAATGG
|| | | ||||| | || || || | | || |||||| ||| | || | | | ||| |||| | || | |||||||||||||||| ||||||||||| || ||||| ||||| |||||||| || || ||||||||||| || ||||| |||||||| || ||||||||||
agagatgcatctcgaaaatcactttgtattattattattatcctattatgctctgtaacacatgta--tacatcagtagtatactaaaagagggctactc---agGTTGGTGACAATGTTGGAGATTGTGCCGCACGAGGGGCTGACCTTTTTGAGAGCATAGCAGCTGAAATTATCAGTGCAATGATACTCGGGGGAACAATGG
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 7
---atttccttgacttgtgcttttgtttctttgtttatactttttctgctcttatacagttatacttccgttggtaccttactggttttgatttaattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATTAGTGCCATGATACTTGGTGGAACAATGG
||||| ||| | ||| || | | | ||| || | || | | || | | | | | ||| | | | | |||||||||||||||| |||||||||||||| ||||| |||||||||||||| || || ||||| ||||| || ||||| ||||||||||| ||||||||||
aatatttctttgctctacaactttacttgcct---tgttcttgttatcctatagttcatcttttgctactatatattcttgtataacaaaagaaactactcagGTTGGTGACAATGTTGGAGATTGTGCTGCCCGAGGCGCTGATCTTTTTGAGAGCATAGCAGCAGAAATTATCAGTGCAATGATACTTGGAGGAACAATGG
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 7
lower sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------------atttccttgact-tgtgctttt--------gtttctttgtttatactttttctgctcttatacagttatacttccgttggtaccttactggttttga-------tttaatttta----agGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATTAGTGCCATGATACTTGGTGGAACAATGG
| || ||||| | |||| || || |||||| | | | || | | | | ||| ||| | | || || | ||| || || ||||||| ||||||||||| || ||||||||| ||||||||||| | ||||||||||| || || ||||| || ||||| |||||||| |||||||||||||
gtatttgatctttgttctttttgtttcttactttcttgattctgtgattcccaaacgtgacatccttgtttggggcatatatcactctacaagggtttgcttgtgttttcgtcatttaggcatttaaagccattttcatcttcttgtagGTTGGAGACAATGTGGGGGACTGTGCTGCTAGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTAGGTGGAACAATGG
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 7
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 8
atttccttgacttgtgcttttgtttctttgtttatactttttctgctcttatacagttatacttccgttggtaccttactggttttgatttaattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATTAGTGCCATGATACTTGGTGGAACAATGG
| | | || | | | |||||| ||| |||| | | | | || | | || | | ||| | || | || ||||||| |||||||| || || || |||||||||||||||||| | ||||||||||| || || ||||| || ||||| ||||||||||| || |||||||
gtattagttctttcatttcacgatcctttgtgtatgattttgtcgggcctggaaccttttgtcatcactgaagcttcact----ctcatctt-cttgcagGTTGGAGACAATGTTGGGGACTGCGCTGCTCGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTTGGGGGTACAATGG
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 7
atttccttgacttgtgcttttgtttctttgtttatactttttctgctcttatacagt-tatacttccgttggtaccttactggttttgatttaattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATTAGTGCCATGATACTTGGTGGAACAATGG
|||| || | | |||| ||| || | | ||| ||||||| | | || | | ||| | | | | | || |||| |||||||| |||||||| || |||||||||||| ||||||||||||| ||||||||||||||||||||||| || ||||| |||||||| |||||||||||||
atttgtttcattggtgcattt-ttcatgtctttgccttttttctaagggaaaaatgtatgtcctttccataacaagagttttccctcttcttcatttgaagGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S105_42V6.2 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------atttccttgacttgtgcttttgtttc---tttgtttatactttttctgc-----------tcttatacagtta-tacttccgttggtaccttactggttttgattta-atttta----agGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATTAGTGCCATGATACTTGGTGGAACAATGG
| | || |||| || || ||| | | ||||||| || | ||| | | ||| ||| || |||| | | | || | | || |||| || ||||| ||||||||||||||||| || ||||| ||| | ||||||||||||||||||||||| || ||||||||||| |||||||| || ||||
gtatgtgtaaatgcgttcttttctgtatctgtaagtgtctagtcgtgtctgttttacttcagcgttggttctagtcctctctatacttgcaatgtcaaatagaatttattaaaaatttagtacgtctattggcagtccagttattgaagcctgtacattggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAAAGTATTGCAGCTGAAATTATCAGTGCCATGATTCTTGGTGGCACCATGG
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S28_200V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------atttccttgacttgtgcttttgtttctttgttt-atactttttctgctcttatacagtta--tacttccgttggtaccttactggttt-tgatttaattttaa----gGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATTAGTGCCATGATACTTGGTGGAACAATGG
|| | |||| ||| | | | |||| | ||| | | || | ||| || ||| || ||||| | | | | || | | | | ||||||||| || ||||||||||||||||| || ||||| ||| | ||||||||||||||||||||||| || ||||||||||| |||||||| |||||||
gtatgctcaaattaatgttattctgtatatgtagttgtctaattttgattattagactggtgtcagttgtagtgtgttggacactagtagagttcatccacatttgagtacctctattggtcttccagttgctgatgcctgtacatcgaagtagGTTGGTGATAACGTGGGAGATTGTGCTGCCCGTGGTGCCGATTTATTTGAAAGTATTGCAGCTGAAATCATCAGTGCCATGATTCTTGGTGGTACAATGG
upper sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 7
lower sequence: EFJ13082 (Selaginella moellendorffii), 3'ss of exon 6
atttccttgacttgtgcttttgtttctttgtttatactttttctgctcttatacagttatacttccgttggtaccttactggttttgatttaatttta-agGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATTAGTGCCATGATACTTGGTGGAACAATGG
|| | || | | | || ||| || | | | ||| ||||||| || ||||| || |||||||||||||| ||||||||| | || ||||||||||| || || |||||||| |||||||| || || || || ||||
--------------------------------------------------gta-aattttgtagtttacgtttagttgatggacttaa--tggtcttacagGTTGGAGATAATGTTGGTGATTGTGCTGCTCGTGGTGCTGATTTATTCGAAAGTATTGCTGCGGAGATAATTAGCGCCATGATTCTGGGAGGCACTATGGMapped 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|193685476|gb|FK625370.1|FK625370EST: AGGGAATACCTGAAGACGACCCTAGGAATCCTGCTGTTATTGCTGATCTG GTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAA
genomic: AGGGAATACCTGAAGACGACCCTAGGAATCCTGCTGTTATTGCTGATCTGgtaattgttt ... taattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAA
EST:
gi|193562236|gb|FK519495.1|FK519495EST: AGGGAATACCTGAAGACGACCCTAGGAATCCTGCTGTTATTGCTGATCTG GTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATTCTTTTTGA
genomic: AGGGAATACCTGAAGACGACCCTAGGAATCCTGCTGTTATTGCTGATCTGgtaattgttt ... taattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGAT-CTTTTTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcttatacagttatacttccgttggtaccttactggttttgatttaattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATTAGTGCCATGATACTTGGTGGAACAATGG
ttttgatttaatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttccttgacttgtgcttttgtttctttgtttatactttttctgctcttatacagttatacttccgttggtaccttactggttttgatttaattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATTAGTGCCATGATACTTGGTGGAACAATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA