RetrogeneDB ID: retro_mmus_788

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:48751869..48753714(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082454
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ddx5
• Ensembl ID: ENSMUSG00000020719
• Aliases: Ddx5, 2600009A06Rik, G17P1, HUMP68, Hlr1, p68
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 [Source:MGI Symbol;Acc:MGI:105037]

Sequence

>retro_mmus_788
ATGTCGAGTTATTCTAGTGACCGAGACCACAGCCGGGATCGAGGGTTTGGTGCACCTCGATTTGGAGGGAGTAGAACAGG
ACCCCTCTCTGGAAAGAAGTTTGGAAATCCTGGGGAGAAACTAGTTAAAAAGAAGTGGAATCTTGATGAGCTGCCCAAAT
TTGAGAAGAATTTTTATCAAGAACACCCTGATTTGGCAAGGCGCACCGCACAAGAGGTTGATACATACAGAAGAAGCAAG
GAAATTACAGTTAGAGGTCACAACTGTCCAAAACCTGTTCTGAAGTTTTATGAAGCAAACTTTCCTGCGAATGTCATGGA
CGTGATTGCAAGGCAGAACTTCACTGAACCCACTGCTATTCAAGCTCAGGGCTGGCCAGTTGCTCTCAGTGGATTGGATA
TGGTTGGAGTAGCTCAGACTGGATCTGGGAAAACACTATCTTATTTGCTGCCTGCCATTGTACACATAATCCACCAGCCA
TTCCTAGAGAGAGGTGATGGGCCTATTTGCTTGGTGCTGGCACCAACTCGAGAACTGGCACAGCAGGTGCAGCAAGTGGC
TGCTGAATATTGTAGAGCTTGTCGCTTGAAGTCTACTTGCATCTATGGTGGTGCTCCCAAAGGACCACAGATTCGTGATT
TGGAAAGAGGCGTGGAAATCTGTATTGCAACACCTGGAAGACTGATTGACTTTTTAGAGTGTGGGAAAACCAATCTGAGA
AGAACAACGTACCTTGTCCTCGATGAAGCTGATAGGATGCTTGATATGGGATTTGAACCCCAGATAAGGAAAATCGTGGA
TCAAATAAGACCTGATAGGCAAACACTAATGTGGAGTGCAACTTGGCCAAAAGAAGTAAGACAGCTTGCTGAAGATTTCC
TGAAAGACTATATTCATATCAATATTGGTGCGCTGGAACTGAGTGCAAACCATAACATTCTCCAGATTGTGGATGTATGT
CATGATGTCGAAAAGGATGAAAAGCTTATTCTTCTGATGGAAGAAATCATGAGTGAGAAGGAGAATAAAACCATTGTTTT
TGTTGAAACCAAAAGAAGATGTGATGAACTTACCAGAAAAATGAGGAGAGATGGGTGGCCTGCCATGGGCATCCATGGTG
ACAAGAGTCAGCAGGAACGTGACTGGGTTCTAAGTGAATTCAAACATGGAAAAGCTTCTATTCTGATTGCTACTGATGTG
GCCTCCAGAGGGCTAGATGTGGAAGATGTGAAATTTGTCATCAATTATGACTACCCTAACTCCTCAGAGGATTATATTCA
TCGAATTGGAAGAACTGCTCGCAGTACCAAAACAGGCACAGCATATACTTTCTTTACACCTAATAACATAAAGCAAGCGA
GCGACCTTATCTCTGTGCTTCGGGAAGCTAATCAAGCAATTAATCCCAAGTTGCTTCAGTTGGTCGAAGACAGAGGTTCA
GGTCGTTCCAGGGGTAGAGGAGGCATGAAGGACGATCGTCGTGACAGATACTCTGCAGGCAAAAGGGGTGGATTTAATAC
CTTTAGAGACAGGGAAAACTATGACAGAGGCTACTCTAATCTGCTTAAGAGAGATTTTGGGGCTAAAACTCAGAATGATG
TTTACAGTACTGCAAATTACACCAATGGGAGCTTTGGAAGTAATTTTGTATCTGCTGGCATACAGACCAGTTTTAGGACT
GGTAATCCAACAGGGACTTACCAGAACGATTATGATAGCACTCAGCAATATGGAAGTAATGTTGCAAATATGCACAATGG
TATGAACCAACAGGCATATGCGTATCCTGCTACCGCAGCTGCTGCGCCTATGATTGGCTATCCCGTGCCAACAGGGTATT
CTCAA

Alignment

ORF - retro_mmus_788 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.05 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSYSSDRDRGRDRGFGAPRFGGSRTGPLSGKKFGNPGEKLVKKKWNLDELPKFEKNFYQEHPDLARRTA
          MSSYSSDRD..RDRGFGAPRFGGSRTGPLSGKKFGNPGEKLVKKKWNLDELPKFEKNFYQEHPDLARRTA
Retrocopy MSSYSSDRDHSRDRGFGAPRFGGSRTGPLSGKKFGNPGEKLVKKKWNLDELPKFEKNFYQEHPDLARRTA

Parental  QEVDTYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQT
          QEVDTYRRSKEITVRGHNCPKPVL.FYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQT
Retrocopy QEVDTYRRSKEITVRGHNCPKPVLKFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQT

Parental  GSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQ
          GSGKTLSYLLPAIVHI.HQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQ
Retrocopy GSGKTLSYLLPAIVHIIHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQ

Parental  IRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSA
          IRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSA
Retrocopy IRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSA

Parental  TWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKDEKLIRLMEEIMSEKENKTIVFVET
          TWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKDEKLI.LMEEIMSEKENKTIVFVET
Retrocopy TWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKDEKLILLMEEIMSEKENKTIVFVET

Parental  KRRCDELTRKMRRDGWPAMGIHGDKSQQERDWVLNEFKHGKAPILIATDVASRGLDVEDVKFVINYDYPN
          KRRCDELTRKMRRDGWPAMGIHGDKSQQERDWVL.EFKHGKA.ILIATDVASRGLDVEDVKFVINYDYPN
Retrocopy KRRCDELTRKMRRDGWPAMGIHGDKSQQERDWVLSEFKHGKASILIATDVASRGLDVEDVKFVINYDYPN

Parental  SSEDYIHRIGRTARSTKTGTAYTFFTPNNIKQVSDLISVLREANQAINPKLLQLVEDRGSGRSRGRGGMK
          SSEDYIHRIGRTARSTKTGTAYTFFTPNNIKQ.SDLISVLREANQAINPKLLQLVEDRGSGRSRGRGGMK
Retrocopy SSEDYIHRIGRTARSTKTGTAYTFFTPNNIKQASDLISVLREANQAINPKLLQLVEDRGSGRSRGRGGMK

Parental  DDRRDRYSAGKRGGFNTFRDRENYDRGYSNLLKRDFGAKTQNGVYSAANYTNGSFGSNFVSAGIQTSFRT
          DDRRDRYSAGKRGGFNTFRDRENYDRGYSNLLKRDFGAKTQN.VYS.ANYTNGSFGSNFVSAGIQTSFRT
Retrocopy DDRRDRYSAGKRGGFNTFRDRENYDRGYSNLLKRDFGAKTQNDVYSTANYTNGSFGSNFVSAGIQTSFRT

Parental  GNPTGTYQNGYDSTQQYGSNVANMHNGMNQQAYAYPATAAAAPMIGYPMPTGYSQ
          GNPTGTYQN.YDSTQQYGSNVANMHNGMNQQAYAYPATAAAAPMIGYP.PTGYSQ
Retrocopy GNPTGTYQNDYDSTQQYGSNVANMHNGMNQQAYAYPATAAAAPMIGYPVPTGYSQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	1.50 RPM	645.89 RPM
SRP007412_cerebellum	1.52 RPM	930.74 RPM
SRP007412_heart	1.12 RPM	347.91 RPM
SRP007412_kidney	1.81 RPM	579.55 RPM
SRP007412_liver	0.66 RPM	372.57 RPM
SRP007412_testis	1.78 RPM	661.48 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_788 was not detected

EST

No EST(s) were mapped for retro_mmus_788 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_12942	149 libraries	311 libraries	564 libraries	38 libraries	10 libraries
TSS #2	TSS_12943	207 libraries	455 libraries	381 libraries	21 libraries	8 libraries

The graphical summary, for retro_mmus_788 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_788 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_788 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019950	1 retrocopy	retro_etel_1009,
Felis catus	ENSFCAG00000003512	1 retrocopy	retro_fcat_172,
Myotis lucifugus	ENSMLUG00000009496	4 retrocopies	retro_mluc_1136, retro_mluc_1499, retro_mluc_1845, retro_mluc_2208,
Monodelphis domestica	ENSMODG00000003743	4 retrocopies	retro_mdom_1519, retro_mdom_1520, retro_mdom_1955, retro_mdom_1956,
Mus musculus	ENSMUSG00000020075	2 retrocopies	retro_mmus_582, retro_mmus_662,
Mus musculus	ENSMUSG00000020076	1 retrocopy	retro_mmus_3362,
Mus musculus	ENSMUSG00000020719	1 retrocopy	retro_mmus_788 ,
Pteropus vampyrus	ENSPVAG00000001932	1 retrocopy	retro_pvam_1267,
Rattus norvegicus	ENSRNOG00000030680	1 retrocopy	retro_rnor_1277,
Tupaia belangeri	ENSTBEG00000009490	1 retrocopy	retro_tbel_4260,
Tarsius syrichta	ENSTSYG00000012149	1 retrocopy	retro_tsyr_1269,
Tursiops truncatus	ENSTTRG00000008793	1 retrocopy	retro_ttru_1662,