RetrogeneDB ID: retro_btau_1217

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:31012305..31013075(+)
• Located in intron of: ENSBTAG00000021602

Retrocopy information

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

Parental gene information

• Parental gene symbol: C10H15ORF23
• Ensembl ID: ENSBTAG00000032340
• Aliases: None
• Description: putative TRAF4-associated factor 1 [Source:RefSeq peptide;Acc:NP_001033144]

Sequence

>retro_btau_1217
TCGGATGAGGCCTGTGGGTGGAAGCAGCAGGTACCTGGGCCCAGCCATGCCACCTTGTTACAATGCCAGCATGGTTAAGA
TGGCATACACCTTGCAGCCCTCCTCTGTGTTAAGTAGTGGCCTGCCCACATACGCACAAACTCAAGACACTTCTAAGAGC
CTATTGCCTGTTAAGTCCAAAGAAGTTGATGCTTCCAGACCTCGTTCAAGAGGTTTGGAGAATGATGTTAGAAAAATCAT
CAGACCAAGACGCGAGAATGGGCAGGTGAAAGCTACAGACACTGCCACCAGGAGGAACATCAGCAAGAGCCACAGATCAC
TTAGTAAACTGAAATCAGAGGAAGAGCTCGAGAATAAGAACCAGCTCTTAAAGGCCATCAACAAGCAGTTGCACCAGAAG
TTGACTGAAACTCAGGGAGAACTGAAGGACCTGACCCAGAAGGTGGAGCTAATGGAGAAGTTTTAGAACAACTGTCGAGC
AGTTTTAGAGGGCAAGGGCCTCAACCCAGGCAGTGAGACCCTGGTATCATACATACCTAGACTCGCCACTACGGATCACA
TGGACTCTACATTGCTGTTAGAAACTTTGCAAGATAAGCTGAAGCTTTTTAACGAAACAGCCAAAAAACAGATGGGAGGA
GTTGCAGGTCTTAAAGGTAAGGCTGAAGATGAAAGAAGACGCCCAGTTCAAAGAACAGCAGACCTTATATAACAGTCAAA
TAAATGATTTTACAACAGCGCTTGAGGAAATGGAGCAGCTATTAGAAATA

Alignment

ORF - retro_btau_1217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.43 %
• Parental protein coverage: 81.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SDEACGQEQQAPGP-QPCRLVTM-TSVVKTVYTLQPSCVLSSGLPADAQTRATFKSQLPVKSKEVDVSRP
          SDEACG..QQ.PGP.QPC.LVTM..S.VK..YTLQPS.VLSSGLP..AQT..T.KS.LPVKSKEVD.SRP
Retrocopy SDEACGWKQQVPGP<QPCHLVTM<ASMVKMAYTLQPSSVLSSGLPTYAQTQDTSKSLLPVKSKEVDASRP

Parental  HSGASENDVTKIIKPRRENGQVKATDTS-RRNLRKSYKPLSKQKSEEELKDKNQLLEAVNKQLHQKLIET
          .S...ENDV.KII.PRRENGQVKATDT..RRN..KS...LSK.KSEEEL..KNQLL.A.NKQLHQKL.ET
Retrocopy RSRGLENDVRKIIRPRRENGQVKATDTATRRNISKSHRSLSKLKSEEELENKNQLLKAINKQLHQKLTET

Parental  QGELKDLTQKVELLEKFQDNCLAILESKGLNPGSETLAS--QQDSTADHVDSMLLLQTLQDELKLFNETA
          QGELKDLTQKVEL.EKF..NC.A.LE.KGLNPGSETL.S......T.DH.DS.LLL.TLQD.LKLFNETA
Retrocopy QGELKDLTQKVELMEKF*NNCRAVLEGKGLNPGSETLVSYIPRLATTDHMDSTLLLETLQDKLKLFNETA

Parental  KKQM-KELQALKVKLKMKEEERAQFLEQQTLCSNQVNDFTTALEEMEQLLEI
          KKQM..ELQ.LKV.LKMKE...AQF.EQQTL...Q.NDFTTALEEMEQLLEI
Retrocopy KKQM>EELQVLKVRLKMKED--AQFKEQQTLYNSQINDFTTALEEMEQLLEI

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	3.46 RPM
ERP005899_muscle	0.05 RPM	13.57 RPM
SRP017611_brain	0.00 RPM	4.34 RPM
SRP017611_kidney	0.06 RPM	4.33 RPM
SRP017611_liver	0.00 RPM	0.91 RPM
SRP030211_testis	0.02 RPM	247.54 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1217 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1217 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000032340	2 retrocopies	retro_btau_1217 , retro_btau_274,
Choloepus hoffmanni	ENSCHOG00000007085	3 retrocopies	retro_chof_1378, retro_chof_2237, retro_chof_504,
Monodelphis domestica	ENSMODG00000000464	1 retrocopy	retro_mdom_1200,
Otolemur garnettii	ENSOGAG00000009825	1 retrocopy	retro_ogar_1829,
Tupaia belangeri	ENSTBEG00000012043	4 retrocopies	retro_tbel_2696, retro_tbel_3958, retro_tbel_4092, retro_tbel_787,
Tursiops truncatus	ENSTTRG00000010577	1 retrocopy	retro_ttru_240,