Sequence
atgc intronic sequence ATGC exonic sequencegttagactcaccagtgtttttcaatgttgaatttcacattcctataagaatttttcataatttggagtgctattgttttttgctcagTTGAAGGATCTCCAGGTTTTCACCATTATCCGTGTTATATTCCAACTTGCTGACGAGATTCCCTGCATTTCTGCTGTTGTTGTTGCCCTACTTGCCGAG
Basic information
species | Glycine max |
transcript | GLYMA18G45720.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G45720.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g22640.4 (Oryza sativa), 3'ss of exon 5
--gttag-actcaccagtgtttttcaatgttgaatt-tcacattcctataagaatttttcataatttggagtgctattgttttttgct------cagTTGAAGGATCTCCAGGTTTTCACCATTATCCGTGTTATATTCCAACTTGCTGACGAGATTCCCTGCATTTCTGCTGTTGTTGTTGCCCTACTTGCCGAG
||| | | || |||||| || | |||| | ||| || | | || | | | | || || | ||| | || ||||| || || | ||||||| |||||||| |||| ||||| | || ||||| || ||||| ||||||||||||||||| || ||||| |||
gttttactatttctttgttcttttcagtgattaattcttacagaagtaaatctctcttgaactagtcatgatatcatctttgccaaccatctcacagCTCAAAGATCTTCAAGTCTACACCATTGTCCGTGTTGTATTTCAACTATCAGAGGAGATCCCTTGCATCTCTGCTGTTGTTGTTGCTCTTCTTGCAGAG
upper sequence: GLYMA18G45720.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G092129_T02 (Zea mays), 3'ss of exon 5
gttagactcaccagtgtttttcaatgttgaatttcacattcctataagaatttttcataatttggagtgctattgttttttgctcagTTGAAGGATCTCCAGGTTTTCACCATTATCCGTGTTATATTCCAACTTGCTGACGAGATTCCCTGCATTTCTGCTGTTGTTGTTGCCCTACTTGCCGAG
||| | ||| || | | | || | || | | ||| ||| | | | || ||| | |||||||| ||||| | || | || ||||||||||| ||||| |||| || || || |||||||||||||||||||| || || ||||| ||
gttttctttgccacaacaatttggga--agacaactgttcttgattataagtccttatattttttacc-taaccatcttg----cagCTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGAT
upper sequence: GLYMA18G45720.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G61050.1 (Arabidopsis thaliana), 3'ss of exon 6
-------gttagactcaccagtgtttttcaatgttgaatttcac--attcctataagaatttttcataatttggagtgctattgttttttgct----cagTTGAAGGATCTCCAGGTTTTCACCATTATCCGTGTTATATTCCAACTTGCTGACGAGATTCCCTGCATTTCTGCTGTTGTTGTTGCCCTACTTGCCGAG
| ||| ||| ||| || | | | | || | || ||| ||| || | | | |||||| | ||| |||||||||||||| || |||||||| || |||||||| || |||||||| || |||||||| || || ||||||||||||||||| |||||||| |||
gttactagagagatattttagtatttgtcgtt-tgggttgtcgtttgtgccaatagagattgagtatctctacaaacac--ttgtttctggctgaaacagTTGAAGGATCTTCAAGTTTTCACAGTTGCACGTGTTATCTTTCAACTTGCGGATGAGATTCCTTGTATATCTGCTGTTGTTGTTGCTCTACTTGCTGAG
upper sequence: GLYMA18G45720.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G61030.1 (Arabidopsis thaliana), 3'ss of exon 5
-------gttagac-tcaccagtgtttttcaatgttgaatttcacattc--ctataagaatttttcataatttggagtgctattgttttttgct----cagTTGAAGGATCTCCAGGTTTTCACCATTATCCGTGTTATATTCCAACTTGCTGACGAGATTCCCTGCATTTCTGCTGTTGTTGTTGCCCTACTTGCCGAG
| ||| | ||| ||| || | | | | || || | | | | || || | | |||||| | ||| |||||||||||||| || |||||||| || |||||||| || |||||||| || |||||||| | || ||||||||||||||||| ||||| || |||
gttactagagagatatttttagtatttgtcgtt-tgggttgtcgttttgtgccaaatagagattgagtatctctacaaacacttgtttctggctgaaacagTTGAAGGATCTTCAAGTTTTCACAGTTGCACGTGTTATCTTTCAACTTGCGGATGAGATTCCTCGTATATCTGCTGTTGTTGTTGCTCTACTGGCTGAG
upper sequence: GLYMA18G45720.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0048g01410.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------gttagactcaccagtgtttttcaatgttgaatttcacattcctataagaatttttcataatttggagtgctattgttttttgctcagTTGAAGGATCTCCAGGTTTTCACCATTATCCGTGTTATATTCCAACTTGCTGACGAGATTCCCTGCATTTCTGCTGTTGTTGTTGCCCTACTTGCCGAG
| || || | ||| | | ||| | | | | | || | | | | | | | | ||| ||||||||||||||||| |||||||| || |||||||| ||||||||||| || ||||| || || |||||||||||| ||||||| |||||| | |||
gttggtgaattattctttccttctttgttccatagtttccatgcctggatatcattttcaaatcctagcatacaacatagatgtaatttgaatcttgttattgtgctgctttctgcagTTGAAGGATCTCCAAGTTTTCACTGTTGCTCGTGTTATCTTCCAACTTGCAGAAGAGATACCTTGTATTTCTGCTGTTATTGTTGCTCTACTTTCTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcacattcctataagaatttttcataatttggagtgctattgttttttgctcagTTGAAGGATCTCCAGGTTTTCACCATTATCCGTGTTATATTCCAACTTGCTGACGAGATTCCCTGCATTTCTGCTGTTGTTGTTGCCCTACTTGCCGAG
ttttttgctc CT-rich tract
tataagaatttttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagactcaccagtgtttttcaatgttgaatttcacattcctataagaatttttcataatttggagtgctattgttttttgctcagTTGAAGGATCTCCAGGTTTTCACCATTATCCGTGTTATATTCCAACTTGCTGACGAGATTCCCTGCATTTCTGCTGTTGTTGTTGCCCTACTTGCCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT