Sequence
atgc intronic sequence ATGC exonic sequence...atccattaaatgtataactatgatcttagatgattgtgtgagcttcttgatcagggttacctatttcttatgctggatttttgtttcccatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGGAACACCGGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
Basic information
species | Glycine max |
transcript | GLYMA14G10950.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g39260.1 (Oryza sativa), 3'ss of exon 6
atccattaaatgtataactatgatcttagatgattgtgtgagcttcttgatcagggttacctatttcttatgctggatttttgtttcccatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGGAACACCGGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
| | | | || | | || ||| | || || | | | || |||||| | || || | | ||||||| ||||| ||||||||| ||| | |||||||||||| | |||||||| || ||||| ||||| |||||||| |||||| |||| | |||||| | |
---------gtaattcttgagaacttttggt-atcatgtttg--tccagactaagatgga--atgtcttatattt-atccttatacacatatggttacagGTCTTGAAGAGTGATGATGTGGATTTGATGATCATTGCCAGGGGAACACCTGGATTCTCAGGTGCAGACCTTGCTAACTTGGTTAATGTGGCTGCTCTTA
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g39250.1 (Oryza sativa), 3'ss of exon 6
atccattaaatgtataactatgatcttagatgattgt--gtgagcttcttgatcagggttacct---atttcttatgctggatttttgtttcccatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGGAACACCGGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
| || | || | | | || | ||| |||| | | | || |||||| | || || | | | ||||||| ||||| ||||||||| ||| | |||||||||||| | |||||||| || ||||| ||||| |||||||| |||||| | || | |||||| | |
-------------------gtaattcttgagaacttttggtatcatgtttgtccaggctaaaatggaatgtcttatagtt-atccttatacacatatgattacagGTCTTGAAGAGTGATGATGTGGATTTGATGATCATTGCCAGGGGAACACCTGGATTCTCAGGTGCAGACCTTGCTAACTTGGTAAATGTGGCTGCTCTTA
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G463032_T01 (Zea mays), 3'ss of exon 5
atccattaaatgtataactatgatcttagatgattgtgtgagcttcttgatcagggttacctatttcttatgctggatttttgtttcccatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGGAACACCGGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
||||||| || | | | || || || | |||| | | | | | | | | | | | ||| | |||| | ||||||||| || ||||||||||||| ||||||||||||| ||||||||||| |||||||| |||||| | || |||||||| | |
-------------------gtgatcttgagaccttttattattttactg-tcccactcgtatattgcctcttaccg-----tcctactcgtttattgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCTAGAGGAACACCGGGATTCTCTGGTGCAGACCTTGCTAACTTGGTAAATGTTGCTGCTCTTA
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G096764_T01 (Zea mays), 3'ss of exon 6
atccattaaatgtataactatgatcttagatgattgt-gtgagcttcttgatcagg-gttacctatttcttatgctggatttttgtttcccatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGGAACACCGGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
|||| | || | | | || | || ||| | | | ||||| | | | | | ||| | | | ||| | |||| | ||||||||| || |||||||||||||| |||||||||| || ||||| ||||| |||||||| |||||| | || ||||||| | |
-------------------gtgattcttgagaactcttgttcctgtgttattcaaatgaaatcgttttctcttaccg---tcctattt---gtttattgcagATCTTGAAAGGTGATGATGTGGACTTAATGATCATTGCCAGAGGAACACCCGGATTCTCCGGTGCAGACCTTGCTAACTTGGTAAATGTTGCTGCACTTA
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------------------------------------------------atccattaaatgtataactatgatcttagat--gattgtgtgagcttcttg-atcagggttacctatttcttatgctggatttttgtttcccatcaaa----tacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGGAACACCGGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
|||| | | | || || | | | ||| || | | |||| |||| | || | ||| | ||| || | | ||||||||||||||| |||||||||||||| ||||| ||||| ||||||| || ||||| || |||||||| |||||||||||| | || ||||||||| |||
gtattgtcaccctctaccaaaaattttaaggtgttttttgtacaatgaacactaagttggagtaaaaaagggctctacttttccagtcttgggaaggctttgcttgtgtgtctatttgcatggctgaccagtatcaaggtt--ttgcttttccccttggcctaatgtatctaaatactattctacagGTTCTGAAGGGGGATGATGTTGATCTGATGATAATTGCTAGAGGAACTCCTGGGTTTTCAGGTGCTGATCTTGCAAACTTGGTCAATATTGCTGCTCTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgatcagggttacctatttcttatgctggatttttgtttcccatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGGAACACCGGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
tcttgat putative branch site (score: 4)
tttttgtttcccatc putative PPT
tatttcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atccattaaatgtataactatgatcttagatgattgtgtgagcttcttgatcagggttacctatttcttatgctggatttttgtttcccatcaaatacagGTTCTGAAGGCTGATGATGTTGATCTAATGATCATTGCCCGAGGAACACCGGGGTTCTCTGGTGCTGACCTTGCAAACTTGATTAACATTGCTGCTATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- ccattaa
- - - - - - - - - - - - - - - - - tgtgtga
- - - - - - - - - - - - - - - - - - - - -gcttctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgga