RetrogeneDB ID: retro_amel_160

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192342.1:301105..302510(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000004851
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000007786
• Aliases: None
• Description: Elongation factor 1-alpha [Source:UniProtKB/TrEMBL;Acc:G1LMH6]

Sequence

>retro_amel_160
AAACCACAGCTAAATGTAAACCAAAACGGGAAAGGAAAAGACACATATTGACATCATCACCACTGGACATGTAGATACAG
GTAAGTTTACCACTACCAGTCATCTGATCTACAAATGTGGTGAAATTGACAAAAGAACTATCAAAAAATTGAGGAGGCTG
CTGAGATGGGAAAGGGCCCCTTCAAGTATGTTTGACTTGGATAAACTGAAAGCTGAACACGAACGTGGTATCACCATTGA
TATCTCCCTGTGGAAATTCGAGACCAGCAAGTATTACATGAGCATAACTGATGTCCCAAGACACAGAGACTTTATCAAAA
ACATGATTCCAGGCACATCTCAGGCTGACTGTGCTGTCCTGATTGTTACTGCTGGTGTTGATGAATTTGAAGCAGGTATC
TCCAAGAATGGGCAGACCTGTGAGCATGCCCTTCTGGCTTACACACTGGGTGTAAAACAACTAATTGTTGGTGTTAACAA
AATGGATTCCACTGAGCCACCCTACAGCCAGAAGAGATAATGAGGAAATCATAAAGGAAGTCAGCACCTACATCAAGAAA
ATTGGCTACAACCCTGACACAGTAGCATTTGTGCCAATTTCTGGTTGGAATGGTGACAACATGCTGGAGCCAAGTGCTAA
CATGCCTTGGTTCAAGGGATGGAAAGTCACCCGTAAAGATGGGAACGCCAGTGGAACCACACTGCTTGAAGCTCTGGATT
GCATTCTGCCACCAACTCACCCAACCGACAAGCCCTTGTGTCTGCCTCTCCAGAACATCTACAAAATTGGTGGTATTGGT
ACTGTTCCTGTGGGCCAAGTGGAGACTAGTGCTCTTAAACCTGGCATGGTGGTCACCTCTGCTCCAGTCAATGTTACAAC
CAAAGTAAAGTCTCTCAATATGCACCATGAAGCTTTGAGTGAGGCTCCTCCTGGGGACAATGTGGGCTTCAATGTCAAAA
ACATATCTGTCAAAGATGTTCATCATGGCAATGTGGCTGGTGACAGCAAAAATGACCACCAAGGGAAGCAGCTGACTTCA
CAGCTCAGGTGATTATCCTGAACCATCTAGGCCAGAGCAGTGCTGGATATGCAACTGTGCTGGATCGTCACACAGCTCAC
ATTGCTTGCAAGTTTGCTGAGCTGAAGGAGAAGATAGATCGTCATTCTGGAAAAAAGCTGGAAGATGGTTGCAAGTTCTT
CAAATCTAGTGATGCTGCCATTGTTGATATGGTTCCTGGCAAGCCTGTGTGTGTTAAGAGCTTCTCTGACTATCCTCCTC
TGGACTGCTTTGCTGTTCGAGACATGAGACAGATGGCTGCTGTGGGTGTCATCAGTGCAGTGGACAAGAAGACAGCTGGA
GCTAGCAAGGTCACCAAGACTGCCCAGAAAGCTCAGAAGTCTAAA

Alignment

ORF - retro_amel_160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.4 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KPPLNLNQN-GKGKDS-HIVVIGHVDSGKSTTTGHLIYKCGGIDKRTI-EKFEKEAAEM-GKGSFKYAWV
          KP.LN.NQN.GK.K....I...GHVD.GK.TTT.HLIYKCG.IDKRTI..K.E.EAAEM.GKG.......
Retrocopy KPQLNVNQN>GKEKTHIDIITTGHVDTGKFTTTSHLIYKCGEIDKRTI<QKIE-EAAEM<GKGPLQVCLT

Parental  -LDKLKAERERGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGIS
          .LDKLKAE.ERGITIDISLWKFETSKYY..I.D.P.HRDFIKNMI.GTSQADCAVLIV.AGV.EFEAGIS
Retrocopy <LDKLKAEHERGITIDISLWKFETSKYYMSITDVPRHRDFIKNMIPGTSQADCAVLIVTAGVDEFEAGIS

Parental  KNGQTREYALLAYTLGVKQLIVGVNKMDSTEPPYSQKR-YEEIVKEVSTYIKKIGYNPDTVAFVPISGWN
          KNGQT.E.ALLAYTLGVKQLIVGVNKMDSTEPPYSQKR..EEI.KEVSTYIKKIGYNPDTVAFVPISGWN
Retrocopy KNGQTCEHALLAYTLGVKQLIVGVNKMDSTEPPYSQKR>NEEIIKEVSTYIKKIGYNPDTVAFVPISGWN

Parental  GDNMLEPSANMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRV
          GDNMLEPSANMPWFKGWKVTRKDGNASGTTLLEALDCILPPT.PTDKPL.LPLQ..YKIGGIGTVPVG.V
Retrocopy GDNMLEPSANMPWFKGWKVTRKDGNASGTTLLEALDCILPPTHPTDKPLCLPLQNIYKIGGIGTVPVGQV

Parental  ETGVLKPGMVVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKND-PPME
          ET..LKPGMVVT.APVNVTT.VKS..MHHEALSEA.PGDNVGFNVKN.SVKDV..GNVAGDSKND.PP.E
Retrocopy ETSALKPGMVVTSAPVNVTTKVKSLNMHHEALSEAPPGDNVGFNVKNISVKDVHHGNVAGDSKND<PPRE

Parental  AAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVP
          AA.FTAQVIILNH.GQ.SAGYA.VLD.HTAHIACKFAELKEKIDR.SGKKLEDG.KF.KS.DAAIVDMVP
Retrocopy AADFTAQVIILNHLGQSSAGYATVLDRHTAHIACKFAELKEKIDRHSGKKLEDGCKFFKSSDAAIVDMVP

Parental  GKPMCVESFSDYPPLGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
          GKP.CV.SFSDYPPL..FAVRDMRQ..AVGVI.AVDKK.AGA.KVTK.AQKAQK.K
Retrocopy GKPVCVKSFSDYPPLDCFAVRDMRQMAAVGVISAVDKKTAGASKVTKTAQKAQKSK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_160 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_160 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007786	14 retrocopies	retro_amel_1064, retro_amel_1072, retro_amel_1079, retro_amel_1140, retro_amel_1167, retro_amel_1203, retro_amel_1227, retro_amel_1283, retro_amel_1371, retro_amel_160 , retro_amel_1742, retro_amel_1797, retro_amel_1855, retro_amel_200,
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Dipodomys ordii	ENSDORG00000009629	1 retrocopy	retro_dord_509,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Erinaceus europaeus	ENSEEUG00000000342	3 retrocopies	retro_eeur_407, retro_eeur_492, retro_eeur_625,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mus musculus	ENSMUSG00000037742	15 retrocopies	retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Ictidomys tridecemlineatus	ENSSTOG00000007687	4 retrocopies	retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,