RetrogeneDB ID: retro_btau_1140

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 28:9034100..9034777(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AHCY
• Ensembl ID: ENSBTAG00000018101
• Aliases: None
• Description: Adenosylhomocysteinase [Source:UniProtKB/Swiss-Prot;Acc:Q3MHL4]

Sequence

>retro_btau_1140
GTGTCAACGACTCCTGACATGATGAATGCGGGCAAGATGGCGGTGGTAGTGGGCTGTGGCAACAAGGGCAATGGCTGTGC
CCAGGCCCTAAGGGATTTCGGGGCCCGATTCATCATAGGAGAGATGAACTCCATCAATGCGCTTTAGGCTGCCATGGAGG
GGTGTGAGGTGACCATCATGGATGAGACCCCTCAGGAGGGCAGCATTTTGTCACCACCATTGGCTGTACCAAGCTCATCC
GTCAACCCACGCTTTGAACAGATGAAAGATGATGTCACTGTGTGTAAATCAGATGCTTTAACGTGGAGATTGATATCAAG
TGCCTGAATGAGAGTACTGTGGAGAAGGCAAACATCAAGCCCCAGGTGGACTGTACTTGTTGAATAATGGGCACTGATCA
TAGGGCTGGCCAAGGGCCAGCTGGTCCACCGGGACTGCACCATGGGCCATCCCAGCTTCATGATGAGCGACTCCTTCACC
AACCAGGTGCTGGCGAAGACTGAGCTGTAGACCCACCCAGATAAACACCCTGTGGAGGTCTACTTCCTGCCCAAGAACCT
GGACAAAGCAGTGGCTGAAGCCCCCCTGGGCAAGCTGAATGTGAAGCTGACCAAGCTGACTGAGAAGCAGGCCCATACCT
GGGCGTGTCCCATGATGGCCTTTTCCAGCCTGACCAC

Alignment

ORF - retro_btau_1140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.38 %
• Parental protein coverage: 52.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  IKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACQEGNI-
          .....D.M.AGK.AVV.G.G..G.GCAQALR.FGAR.II.E...INAL.AAMEG.EVT.MDE..QEG.I.
Retrocopy VSTTPDMMNAGKMAVVVGCGNKGNGCAQALRDFGARFIIGEMNSINAL*AAMEGCEVTIMDETPQEGSI<

Parental  FVTTTGCTDII-LGQHFEQMKDDAIVCN-IGHFDVEIDVKWLNENAVEKVNIKPQVD-RYLLKNGR-RII
          FVTT.GCT..I.....FEQMKDD..VC..I..F.VEID.K.LNE..VEK.NIKPQVD..YLL.NG...II
Retrocopy FVTTIGCTKLI>VNPRFEQMKDDVTVCK<IRCFNVEIDIKCLNESTVEKANIKPQVD<LYLLNNGH<LII

Parental  LLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLT
          .LA.G.LV...C.MGHPSF.MS.SFTNQVLA..EL.THPDK.PV.V.FLPK.LD.AVAEA.LGKLNVKLT
Retrocopy GLAKGQLVHRDCTMGHPSFMMSDSFTNQVLAKTEL*THPDKHPVEVYFLPKNLDKAVAEAPLGKLNVKLT

Parental  KLTEKQAQ-YLGVSREGPFKPDH
          KLTEKQA..YLGVS..G.F.PDH
Retrocopy KLTEKQAH<YLGVSHDGLFQPDH

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	1120.08 RPM
ERP005899_muscle	0.05 RPM	454.04 RPM
SRP017611_brain	0.00 RPM	51.30 RPM
SRP017611_kidney	0.00 RPM	359.25 RPM
SRP017611_liver	0.00 RPM	1012.04 RPM
SRP030211_testis	0.03 RPM	32.33 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1140 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1140 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1140 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018101	1 retrocopy	retro_btau_1140 ,
Canis familiaris	ENSCAFG00000007504	2 retrocopies	retro_cfam_1486, retro_cfam_552,
Echinops telfairi	ENSETEG00000002576	1 retrocopy	retro_etel_444,
Gorilla gorilla	ENSGGOG00000014694	5 retrocopies	retro_ggor_1148, retro_ggor_1795, retro_ggor_2822, retro_ggor_3087, retro_ggor_511,
Monodelphis domestica	ENSMODG00000002753	1 retrocopy	retro_mdom_1974,
Mus musculus	ENSMUSG00000027597	1 retrocopy	retro_mmus_197,
Nomascus leucogenys	ENSNLEG00000010041	4 retrocopies	retro_nleu_1717, retro_nleu_2785, retro_nleu_40, retro_nleu_929,
Oryctolagus cuniculus	ENSOCUG00000008592	1 retrocopy	retro_ocun_1886,
Rattus norvegicus	ENSRNOG00000017777	7 retrocopies	retro_rnor_1142, retro_rnor_1820, retro_rnor_1903, retro_rnor_2120, retro_rnor_569, retro_rnor_647, retro_rnor_839,
Sus scrofa	ENSSSCG00000007278	1 retrocopy	retro_sscr_119,
Xenopus tropicalis	ENSXETG00000019486	1 retrocopy	retro_xtro_62,