RetrogeneDB ID: retro_btau_1636

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:15958444..15958898(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPC
• Ensembl ID: ENSBTAG00000024549
• Aliases: SNRPC, U1C
• Description: U1 small nuclear ribonucleoprotein C [Source:UniProtKB/Swiss-Prot;Acc:Q32PA0]

Sequence

>retro_btau_1636
TTTTATTGTGACTACTGTGATCCATTCCTCACCCACGATTCTGCCTCTGTGAGAAAGACACACTGCAGTGGTAGGAAGCA
CGAAGAGAATGTGAAGGACTACTATCAGAAATGCATAGAAGGGCAGGCTCAGAGCCTGATTGATAAAAACAACAGCTATT
TCAACAAGGAAAGATACCTTTTATTCCATTCTCTGCTCCTCCTCCTGCAGGGGCAATGATCCCACCTCCCCCCAGTCTCC
CAGGACCTCCTGCCCAGGGATGAAGCTAGCACCCCACATGGGGGTCCCTCCCATGATGCCAATGATGAGCCCTCCTCCTC
CTGGGATCATGCCAGTGGGACCTGCTCCTAGAATGAGGCTGCCTATGGGAGGCCACATACCCATGATGCCTGGACCCCCA
GTGATGAGACCTTCTGCCTGTCTCATCATGGTGCCCACCTGGTGAGGAAAGACC

Alignment

ORF - retro_btau_1636 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.22 %
• Parental protein coverage: 95.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTA-AFQQGKIPPTPFSAPPP
          FYCDYCD..LTHDS.SVRKTHCSGRKH.ENVKDYYQK..E.QAQSLIDK.....FQQGKIP..PFSAPPP
Retrocopy FYCDYCDPFLTHDSASVRKTHCSGRKHEENVKDYYQKCIEGQAQSLIDKNNS<LFQQGKIPFIPFSAPPP

Parental  AGAMIPPPPSLPGPPR-PGMMPAPHMGGPPMMPMMGPPPPGMMPVGPAPGMRPPMGGHMPMMPGPPMMRP
          AGAMIPPPPSLPGPP..PGM..APHMG.PPMMPMM.PPPPG.MPVGPAP.MR.PMGGH.PMMPGPP.MRP
Retrocopy AGAMIPPPPSLPGPPA<PGMKLAPHMGVPPMMPMMSPPPPGIMPVGPAPRMRLPMGGHIPMMPGPPVMRP

Parental  PARPMMVPTRPGMT
          .A...MVPT..G.T
Retrocopy SACLIMVPTW*GKT

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	12.47 RPM
ERP005899_muscle	0.00 RPM	24.76 RPM
SRP017611_brain	0.05 RPM	11.65 RPM
SRP017611_kidney	0.00 RPM	15.88 RPM
SRP017611_liver	0.00 RPM	16.01 RPM
SRP030211_testis	0.00 RPM	35.38 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1636 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1636 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1636 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000024549	1 retrocopy	retro_btau_1636 ,
Canis familiaris	ENSCAFG00000001231	3 retrocopies	retro_cfam_348, retro_cfam_402, retro_cfam_409,
Callithrix jacchus	ENSCJAG00000015321	16 retrocopies	retro_cjac_1009, retro_cjac_1015, retro_cjac_1064, retro_cjac_1750, retro_cjac_1937, retro_cjac_2014, retro_cjac_2395, retro_cjac_2456, retro_cjac_2785, retro_cjac_3056, retro_cjac_3110, retro_cjac_400, retro_cjac_4010, retro_cjac_617, retro_cjac_770, retro_cjac_873,
Homo sapiens	ENSG00000124562	6 retrocopies	retro_hsap_1531, retro_hsap_1866, retro_hsap_2865, retro_hsap_3195, retro_hsap_3829, retro_hsap_4241,
Loxodonta africana	ENSLAFG00000013534	2 retrocopies	retro_lafr_621, retro_lafr_878,
Monodelphis domestica	ENSMODG00000013904	1 retrocopy	retro_mdom_22,
Nomascus leucogenys	ENSNLEG00000008392	2 retrocopies	retro_nleu_2129, retro_nleu_99,
Oryctolagus cuniculus	ENSOCUG00000026668	3 retrocopies	retro_ocun_1019, retro_ocun_184, retro_ocun_196,
Otolemur garnettii	ENSOGAG00000008755	9 retrocopies	retro_ogar_1040, retro_ogar_130, retro_ogar_1763, retro_ogar_183, retro_ogar_2434, retro_ogar_3064, retro_ogar_3322, retro_ogar_3377, retro_ogar_697,
Pongo abelii	ENSPPYG00000017272	4 retrocopies	retro_pabe_1271, retro_pabe_3066, retro_pabe_3225, retro_pabe_915,
Sarcophilus harrisii	ENSSHAG00000000945	1 retrocopy	retro_shar_112,