RetrogeneDB ID: retro_btau_612

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:12657200..12657953(+)
• Located in intron of: ENSBTAG00000016703

Retrocopy information

• Ensembl ID: ENSBTAG00000047703
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CNN2
• Ensembl ID: ENSBTAG00000020764
• Aliases: None
• Description: Calponin-2 [Source:UniProtKB/Swiss-Prot;Acc:Q3SYU6]

Sequence

>retro_btau_612
GAGGAGGTGGAGCTCTAAAGCCAGATTGAGGACTGACCGGCCTCTCCATCAACCCGGACTTCCAGAAGGGTCTGAAGGAC
GGGACCATCCTGTGCACATGCATGAATAAACTGCAGCTGGGCTCAACCCCTAAGACCAACCGCTCCATGCAGAAGTGGCA
CCAGCTAGAAAACCTCTCCAACTTCATCAAGGCCATGGTCAGCTACAGCATGAACCCCGCTGACCTGTTGGAGGCTAACG
ACTTGTTTGAAAGTGGGAACTTGATGCAGGTGCAGGTGTCTCTTTCTTGCCCTGGCCAGGAAGGCCAAGACAAAGGGGAT
GCAGAGCGGCGTGGACACTGGCATCAAATACTTGGAGAAGTAGGGGCGAGACTCTGATGATGCCACCGTGAAGATGGGCC
AGTGCGTCATTGGGTTCCTGTTGGGCACTAACAAATGTGCCAGCCAGTCGGACATGACCGCTTCTGGCACCAGATGGCAT
CTGTATGACCCCAAAAACCATATCCTGCCCCCCATGGACCACTTGACCATCAGCCTCCAGTTGGGCACAAATAAGTGTGA
CAGCCAGGTGGGCACGACGGCTCCAGGGACCCGGTGGCACATTTACAACACAAAGCTGGGGACAGACAAATGTGACAATT
CCTCCATGTCCCTACAGATGGGCTACATGCAGGGTGCCAACCAGAGTGGTTAGGTCTTTGGCCTGGGCTGGCAGATATAC
GACCCCAAGTACTGCCCTCAGGGCCCAGTGGCA

Alignment

ORF - retro_btau_612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.21 %
• Parental protein coverage: 87.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KEAELRSWIE-GLTGLSVGPDFQKGLKDGIILCTLMNKLQPGSVPKINRSMQNWHQLENLSNFIKAMVSY
          .E.EL.S.IE.GLTGLS..PDFQKGLKDG.ILCT.MNKLQ.GS.PK.NRSMQ.WHQLENLSNFIKAMVSY
Retrocopy EEVEL*SQIE<GLTGLSINPDFQKGLKDGTILCTCMNKLQLGSTPKTNRSMQKWHQLENLSNFIKAMVSY

Parental  GMNPVDLFEANDLFESGNLTQVQVSL-LALAGKAKTKGLQSGVDIGVKYSEKQERNFDDATMKAGQCVIG
          .MNP.DL.EANDLFESGNL.QVQVSL.LALA.KAKTKG.QSGVD.G.KY.EK..R..DDAT.K.GQCVIG
Retrocopy SMNPADLLEANDLFESGNLMQVQVSL>LALARKAKTKGMQSGVDTGIKYLEK*GRDSDDATVKMGQCVIG

Parental  LQMGTNKCASQSGMTAYGTRRHLYDPKNHILPPMDHSTISLQMGTNKCASQVGMTAPGTRRHIYDTKLGT
          ...GTNKCASQS.MTA.GTR.HLYDPKNHILPPMDH.TISLQ.GTNKC.SQVG.TAPGTR.HIY.TKLGT
Retrocopy FLLGTNKCASQSDMTASGTRWHLYDPKNHILPPMDHLTISLQLGTNKCDSQVGTTAPGTRWHIYNTKLGT

Parental  DKCDNSSMSLQMGYTQGANQSGQVFGLGRQIYDPKYCPQGPAA
          DKCDNSSMSLQMGY.QGANQSG.VFGLG.QIYDPKYCPQGP.A
Retrocopy DKCDNSSMSLQMGYMQGANQSG*VFGLGWQIYDPKYCPQGPVA

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	3.60 RPM
ERP005899_muscle	0.48 RPM	28.35 RPM
SRP017611_brain	0.09 RPM	3.97 RPM
SRP017611_kidney	0.24 RPM	32.24 RPM
SRP017611_liver	0.00 RPM	4.30 RPM
SRP030211_testis	0.20 RPM	17.97 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_612 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_612 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002068	1 retrocopy	retro_btau_1701,
Bos taurus	ENSBTAG00000020345	1 retrocopy	retro_btau_1211,
Bos taurus	ENSBTAG00000020764	1 retrocopy	retro_btau_612 ,
Gorilla gorilla	ENSGGOG00000028153	9 retrocopies	retro_ggor_1199, retro_ggor_1271, retro_ggor_1555, retro_ggor_1612, retro_ggor_1646, retro_ggor_1922, retro_ggor_2370, retro_ggor_305, retro_ggor_762,
Macaca mulatta	ENSMMUG00000015306	1 retrocopy	retro_mmul_1131,
Pongo abelii	ENSPPYG00000009302	12 retrocopies	retro_pabe_1299, retro_pabe_1397, retro_pabe_1838, retro_pabe_1920, retro_pabe_2171, retro_pabe_2249, retro_pabe_2900, retro_pabe_3512, retro_pabe_3515, retro_pabe_3543, retro_pabe_3823, retro_pabe_407,