Sequence
atgc intronic sequence ATGC exonic sequencegtgagtactatgaatgcaaatatggatgtgcagaaatatacgtattgtcaaattctaaatattattctactcttcttcagGCACCCTTCCCCTTCAGTGCTTATTCCTGCTCTTCGTACCGTTGGAAATATTGTTACTGGAGATGATTTGCAGACAGAG
Basic information
species | Glycine max |
transcript | GLYMA19G41770.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G41770.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 6
--------------------gtgagtactatgaatgcaaatatggatgtgcaga-aatatacgtattgtcaaattctaaatattattctactcttc------ttcagGCACCCTTCCCCTTCAGTGCTTATTCCTGCTCTTCGTACCGTTGGAAATATTGTTACTGGAGATGATTTGCAGACAGAG
| | || | | ||| | || | ||| | || | |||||| || |||| || | || || || || |||||||||||||| || || || || || |||||||||||||| ||||||||||| ||| || ||
gtaagtgacaacattgcattacaattttctgccattttcctttagattcttatttgctactctcattataccctttttaatatt-ttatactgtttacaacatgaagCCATCCATCACCTTCAGTGCTTATACCCGCACTACGAACTGTTGGAAATATTGTAACTGGAGATGACGCGCAAACTCAG
upper sequence: GLYMA19G41770.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 6
-------------------------------gtgagtactatgaatgcaaatatggatgtgcagaaatatacgtattgtcaaattctaaatattattctactcttcttcagGCACCCTTCCCCTTCAGTGCTTATTCCTGCTCTTCGTACCGTTGGAAATATTGTTACTGGAGATGATTTGCAGACAGAG
||| |||| || | | | | | |||| | | | || | | || | | | | ||| | | ||| || || || || || |||||||| |||||||| || || ||||| |||||||| ||||||||||||||||| || ||
gtatgtgaaaatgatgtgtaacaacttcatgttgattacttcgatagtttttgttgtt-tgcaccagtttttttaatcttgtatatgatgtgtgctgatac-cacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATATTGTCACTGGAGATGATTTGCAAACTCAG
upper sequence: GLYMA19G41770.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0060g01510.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------gtgagtactatgaatgcaaatatggatgtgcagaaatatacgtattgtcaaattctaaatattattctactcttct-tcagGCACCCTTCCCCTTCAGTGCTTATTCCTGCTCTTCGTACCGTTGGAAATATTGTTACTGGAGATGATTTGCAGACAGAG
| | | || || | ||| | || ||| || || | | | | ||| |||| ||||| || ||||| || || |||||||| ||||| || |||||||| ||||| |||||||||||| |||| || ||
gtgagtttttagaaattttgagttagttctggacttcttttggctgtgggatgtgttgtttccattaatttgtacc-tcgggcctgaacttctttcttggactttggtcagTCACCCATCTCCTTCTGTTCTCATTCCTGCACTTCGCACGGTTGGAAACATTGTCACTGGAGATGATATGCAAACCCAG
upper sequence: GLYMA19G41770.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ31559 (Selaginella moellendorffii), 3'ss of exon 2
gtgagtactatgaatgcaaatatggatgtgcagaaatatacgtattgtcaaattctaaatattattctactctt--cttcagGCACCCTTCCCCTTCAGTGCTTATTCCTGCTCTTCGTACCGTTGGAAATATTGTTACTGGAGATGATTTGCAGACAGAG---------------------
|| || | | || | || ||| | | || | | |||| | ||||| || || |||||||||||||||||||| || ||||| ||||| ||||| || ||| | || || ||
---------------------------gta-agtcgtgtctttagctctgacttttaactggcctgacgttcctggttccagGTATCCTTCACCGAATGTTCTTATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGGAAAACTTGAAACGGAACAAC
upper sequence: GLYMA19G41770.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ38593 (Selaginella moellendorffii), 3'ss of exon 6
gtgagtactatgaatgcaaatatggatgtgcagaaatatacgtattgtcaaattctaaatattattctactctt--cttcagGCACCCTTCCCCTTCAGTGCTTATTCCTGCTCTTCGTACCGTTGGAAATATTGTTACTGGAGATGATTTGCAGACAGAG
|| || | | || | || ||| | | || | | |||| | ||||| || || |||||||||||||||||||| || ||||| ||||| ||||| || ||| | || || ||
---------------------------gta-agtcgtgtctttagctctgacttttaactggcctgacgttcctggttccagGTATCCTTCACCGAATGTTCTTATTCCTGCTCTTCGTACGGTGGGAAACATTGTGACTGGTGACGATGTCCAAACGCAGMapped 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|7588820|gb|AW704607.1|AW704607EST: CAAGGTGTAATTGAAGCTGGTGTTTGTAGCCGGCTTGTTGAGCTTCTATT GCACCCTTCCCCTTCAGTGCTTATTCCTGCTCTTCGTACCGTTGGAAATAT
genomic: CAAGGTGTAATTGAAGCTGGTGTTTGTAGCCGGCTTGTTGAGCTTCTATTgtgagtacta ... tcttcttcagGCACCCTTCCCCTTCAGTGCTTATTCCTGCTCTTCGTACCGTTGGAAATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtgcagaaatatacgtattgtcaaattctaaatattattctactcttcttcagGCACCCTTCCCCTTCAGTGCTTATTCCTGCTCTTCGTACCGTTGGAAATATTGTTACTGGAGATGATTTGCAGACAGAG
ttctaaa putative branch site (score: 2)
ttattctactcttctt putative PPT
tattgtcaaattctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtactatgaatgcaaatatggatgtgcagaaatatacgtattgtcaaattctaaatattattctactcttcttcagGCACCCTTCCCCTTCAGTGCTTATTCCTGCTCTTCGTACCGTTGGAAATATTGTTACTGGAGATGATTTGCAGACAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG