Sequence
atgc intronic sequence ATGC exonic sequencegttactagagagatatttttagtatttgtcgtttgggttgtcgttttgtgccaaatagagattgagtatctctacaaacacttgtttctggctgaaacagTTGAAGGATCTTCAAGTTTTCACAGTTGCACGTGTTATCTTTCAACTTGCGGATGAGATTCCTCGTATATCTGCTGTTGTTGTTGCTCTACTGGCTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G61030.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G61030.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G40290.1 (Glycine max), 3'ss of exon 6
gttactagagagatatttttagtatttgtcgtttgggttgtcgttttgtgccaaatagagattgagtatctctacaaacacttgtttctggctgaaacagTTGAAGGATCTTCAAGTTTTCACAGTTGCACGTGTTATCTTTCAACTTGCGGATGAGATTCCTCGTATATCTGCTGTTGTTGTTGCTCTACTGGCTGAG
| ||| | ||| ||| || | | || || | | || | || | | | | | || || | |||||||||||||| || |||||||| || |||||||| || |||||||| ||||||||||| | || ||||||||||| ||||| ||||| ||||||
-------gttagac-tcaccagtgtttttccatgttgaattcacattcctataggaaatttttcaaaattttgagtgttattggcttttgctt----cagTTGAAGGATCTCCAGGTTTTCACCATTATCCGTGTTATATTCCAACTTGCTGATGAGATTCCCTGCATTTCTGCTGTTGTCGTTGCCCTACTTGCTGAG
upper sequence: AT3G61030.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G45720.1 (Glycine max), 3'ss of exon 5
gttactagagagatatttttagtatttgtcgtt-tgggttgtcgttttgtgccaaatagagattgagtatctctacaaacacttgtttctggctgaaacagTTGAAGGATCTTCAAGTTTTCACAGTTGCACGTGTTATCTTTCAACTTGCGGATGAGATTCCTCGTATATCTGCTGTTGTTGTTGCTCTACTGGCTGAG
| ||| | ||| ||| || | | | | || || | | | | || || | | |||||| | ||| |||||||||||||| || |||||||| || |||||||| || |||||||| || |||||||| | || ||||||||||||||||| ||||| || |||
-------gttagac-tcaccagtgtttttcaatgttgaatttcacattc--ctataagaatttttcataatttggagtgctattgttttttgct----cagTTGAAGGATCTCCAGGTTTTCACCATTATCCGTGTTATATTCCAACTTGCTGACGAGATTCCCTGCATTTCTGCTGTTGTTGTTGCCCTACTTGCCGAG
upper sequence: AT3G61030.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G02370.2 (Glycine max), 3'ss of exon 5
-----------------------------------gttactagagagatatttttagtatttgtcgtttgggttg-tcgttttgtgcca-aatagagattgagtatctctacaa-------acacttgtttctggctgaaa-------cagTTGAAGGATCTTCAAGTTTTCACAGTTGCACGTGTTATCTTTCAACTTGCGGATGAGATTCCTCGTATATCTGCTGTTGTTGTTGCTCTACTGGCTGAG
| | | ||| || | | | ||| | || || | ||| || ||| | | | | ||||| | ||| | | |||| |||||||||||||| || |||||||| ||| ||||| || ||||||||||| || ||||| || | || |||||||||||||| ||||| || ||||||
gtaagacttaaccgaatcataatttcatcaatccctattttgttgcatcattcctattgtg-gctgttgaagctgctcttgttgcatcataatttcgtcacattccttttacaatttgtaaaaactgaagttttattgaattttgtttcagTTGAAGGATCTACAGGTTTTCACCATTGTCCGTGTGATATTTCAACTTGCTGAAGAGATCCCCTGCATTTCTGCTGTTGTTGTAGCTCTGCTTGCTGAG
upper sequence: AT3G61030.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G09070.1 (Glycine max), 3'ss of exon 6
----------------------------------------------gttactagagagatatttttagtatttgtcgtttgggttgtcgttttgtgccaaatagagattgagtatctcta--caaacacttgtttctggctgaaacagTTGAAGGATCTTCAAGTTTTCACAGTTGCACGTGTTATCTTTCAACTTGCGGATGAGATTCCTCGTATATCTGCTGTTGTTGTTGCTCTACTGGCTGAG
| | | | | || | | ||| | | ||||||| || | | | | || || || | |||||||||||||| || |||||||| ||| ||||| || || |||||||| || ||||| ||| | || |||||||||||||| ||||| || ||||||
gtaagacttagctgaatcataatttcatcaatccctattttgttgcatcaacccattgggctgttgaagctgcacttgttgcatcataattttgtgacattcctttcacaaattttaaaaattgaagttttattgtcttttctttcagTTGAAGGATCTACAGGTTTTCACCATTGTCCGTGTGATATTCCAACTTGCTGAAGAGATCCCTTGCATTTCTGCTGTTGTTGTAGCTCTGCTTGCTGAG
upper sequence: AT3G61030.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv15s0048g01410.t01 (Vitis vinifera), 3'ss of exon 6
--------gttactagagagatattt--ttagtatttgtcgt-ttgggttgtcgttttgtg--ccaaatagagattgagtatctctacaaacacttgtttctg-gctgaa----acagTTGAAGGATCTTCAAGTTTTCACAGTTGCACGTGTTATCTTTCAACTTGCGGATGAGATTCCTCGTATATCTGCTGTTGTTGTTGCTCTACTGGCTGAG
||| | | ||| | || || | | || | || |||| || | | | | || | | |||||| || |||| |||||||||||||| ||||||||||| ||||| ||||||||||| |||||||| || ||||| ||| |||| ||||||||| ||||||||||||| |||||
gttggtgaattattctttccttctttgttccatagtttccatgcctggatatcattttcaaatcctagcatacaacatagatgtaatttgaatcttgttattgtgctgctttctgcagTTGAAGGATCTCCAAGTTTTCACTGTTGCTCGTGTTATCTTCCAACTTGCAGAAGAGATACCTTGTATTTCTGCTGTTATTGTTGCTCTACTTTCTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgccaaatagagattgagtatctctacaaacacttgtttctggctgaaacagTTGAAGGATCTTCAAGTTTTCACAGTTGCACGTGTTATCTTTCAACTTGCGGATGAGATTCCTCGTATATCTGCTGTTGTTGTTGCTCTACTGGCTGAG
aaataga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttactagagagatatttttagtatttgtcgtttgggttgtcgttttgtgccaaatagagattgagtatctctacaaacacttgtttctggctgaaacagTTGAAGGATCTTCAAGTTTTCACAGTTGCACGTGTTATCTTTCAACTTGCGGATGAGATTCCTCGTATATCTGCTGTTGTTGTTGCTCTACTGGCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT