RetrogeneDB ID: retro_btau_396

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:26388755..26390048(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RNF38
• Ensembl ID: ENSBTAG00000005519
• Aliases: None
• Description: RING finger protein 38 [Source:RefSeq peptide;Acc:NP_001029753]

Sequence

>retro_btau_396
ATGCGACCATGGGAGATGACATCAAATAGGCAGCCCCCTTCAGTTTGACCAAGCCAACATCACTTCTCAGGGGAACGATG
CAACACACCTGCACGCAACAGAAGTTCTCCTGTCAGGCGTCAGAGAGGAAGAAGGGATCGTCAGTCTCGACTTAATTCCA
TTAGTCAAGATGAAAATTATCACCATCTCCCTTATGCACAGCAGCAAGCAATAGAAGAACCTCAAGCCTTCCACCCTCCG
AATGTATCTCCCCGTCTGTTACACCCTGCTGCTCATCCACCCCAGCAGAATGCAGTAGTGGTTGACATACATGATCAGCT
CCATCAGGGCACCGTCCCTGTTTCTTACACAGTAACAACAGTGGCACCACATGGGATTCCCCTCTGCACAGGCCAGCACA
TCCCTGCTTGCAGTACACAACAGGTCCCAGGATGCTCTGTGGTTTTCAGTGGACAGCACCTCCCTGTCTGTAGTGTGCCT
CCTCCAATGCTTCAAGCATGTTCTGTTCAGCACTTACCAGTACCATATGCTGCATTTCCACCCCTTATTTCCAGTGATCC
GTTTATTTTACATCCTCCCCATCTTTCTCCCCATCATCCTCCTCATTTGCCACCTCCAAGCCAGTTTGTCCCTTTCCAAA
CACAGCAGTCACGATCGCCTCTGCAAAGGATAGAAAACGAAGTGGAACTCTTAGGAGAACATCTTCCTGTGGGAGGTTTT
ACTTACCCTCCATCTGCCCATCCCCCGACATTACCTCCATCAGCTCCTTTGCAGTTCCTAACACATGATCCTTTGCATCA
GGAGGTTTCGTATGGAGTACCTTATCCTCCATTTATGCCTCGGAGGCTCACAGGACACAGTAGATACCGATCCCAGCAGC
CCATACCACCACCCCCTTACCATCCCAGCTTACTACCATATGTGTTATCAATGCTTCCAGTGCCACCTGCAGTGGGCCCA
ACTTTCAGCTTTGAATTGGATGTGGAAGATGGAGAAGTAGAAAATTACGAGGCCCTGTTAAACCTAGCAGAGCGACTGGG
AGAGGCCAAGCCTCGAGGACTGACTAAAGCAGATATTGAACAACTTCCTTCTTACCGGTTCAATCCTAACAACCACCAGT
AAGAACAGACTTTGTGTGTAGTATGCATGTGTGATTTTGAGTCAAGGCAGCTACTTAGAGTTTTACCCTGTAACCATGAG
TTCCATGCCAAGTGTGTCGACAAATGGCTTAAGGCAAATCATACTTGCCCAATCTGCCGAGCTGATGCTTCAGAAGTGCA
TCGGGATTCAGAA

Alignment

ORF - retro_btau_396 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRPWEMTSNRQPPSVRPSQHHFSGERCNTPARNRRSPPVRRQRGRRDRQSRLNSISQDENYHHLPYAQQQ
          MRPWEMTSNRQPPSV.PSQHHFSGERCNTPARNR.SP.VRRQRGRRDRQSRLNSISQDENYHHLPYAQQQ
Retrocopy MRPWEMTSNRQPPSV*PSQHHFSGERCNTPARNRSSP-VRRQRGRRDRQSRLNSISQDENYHHLPYAQQQ

Parental  AIEEPRAFHPPNVSPRLLHPAAHPPQQNAVMVDIHDQLHQGTVPVSYTVTTVAPHGIPLCTGQHIPACST
          AIEEP.AFHPPNVSPRLLHPAAHPPQQNAV.VDIHDQLHQGTVPVSYTVTTVAPHGIPLCTGQHIPACST
Retrocopy AIEEPQAFHPPNVSPRLLHPAAHPPQQNAVVVDIHDQLHQGTVPVSYTVTTVAPHGIPLCTGQHIPACST

Parental  QQVPGCSVVFSGQHLPVCSVPPPMLQACSVQHLPVPYAAFPPLISSDPFILHPPHLSPHHPPHLPPPSQF
          QQVPGCSVVFSGQHLPVCSVPPPMLQACSVQHLPVPYAAFPPLISSDPFIL............LPPPSQF
Retrocopy QQVPGCSVVFSGQHLPVCSVPPPMLQACSVQHLPVPYAAFPPLISSDPFILXXXXXXXXXXXXLPPPSQF

Parental  VPFQTQQSRSPLQRIENEVELLGEHLPVGGFTYPPSAHPPTLPPSAPLQFLTHDPLHQEVSYGVPYPPFM
          VPFQTQQSRSPLQRIENEVELLGEHLPVGGFTYPPSAHPPTLPPSAPLQFLTHDPLHQEVSYGVPYPPFM
Retrocopy VPFQTQQSRSPLQRIENEVELLGEHLPVGGFTYPPSAHPPTLPPSAPLQFLTHDPLHQEVSYGVPYPPFM

Parental  PRRLTGRSRYRSQQPIPPPPYHPSLLPYVLSMLPVPPAVGPTFSFELDVEDGEVENYEALLNLAERLGEA
          PRRLTG.SRYRSQQPIPPPPYHPSLLPYVLSMLPVPPAVGPTFSFELDVEDGEVENYEALLNLAERLGEA
Retrocopy PRRLTGHSRYRSQQPIPPPPYHPSLLPYVLSMLPVPPAVGPTFSFELDVEDGEVENYEALLNLAERLGEA

Parental  KPRGLTKADIEQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPIC
          KPRGLTKADIEQLPSYRFNPNNHQ.EQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKAN.TCPIC
Retrocopy KPRGLTKADIEQLPSYRFNPNNHQ*EQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANHTCPIC

Parental  RADASEVHRDSE
          RADASEVHRDSE
Retrocopy RADASEVHRDSE

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
ERP005899_liver	0.00 RPM	2.67 RPM
ERP005899_muscle	0.11 RPM	16.52 RPM
SRP017611_brain	0.18 RPM	18.13 RPM
SRP017611_kidney	0.06 RPM	15.94 RPM
SRP017611_liver	0.00 RPM	2.72 RPM
SRP030211_testis	2.78 RPM	174.37 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_396 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_396 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_396 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005519	1 retrocopy	retro_btau_396 ,
Callithrix jacchus	ENSCJAG00000010299	1 retrocopy	retro_cjac_2182,
Monodelphis domestica	ENSMODG00000002665	1 retrocopy	retro_mdom_1075,